M430 Microarray Eye PDNN Nov05 / WebQTL

From ea46f42ee640928b92947bfb204c41a482d80937 Mon Sep 17 00:00:00 2001 From: root Date: Tue, 8 May 2012 18:39:56 -0500 Subject: Add all the source codes into the github. --- web/dbdoc/EYE_M2_1105_P.html | 287 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 287 insertions(+) create mode 100755 web/dbdoc/EYE_M2_1105_P.html (limited to 'web/dbdoc/EYE_M2_1105_P.html') diff --git a/web/dbdoc/EYE_M2_1105_P.html b/web/dbdoc/EYE_M2_1105_P.html new file mode 100755 index 00000000..a803d650 --- /dev/null +++ b/web/dbdoc/EYE_M2_1105_P.html @@ -0,0 +1,287 @@ + +M430 Microarray Eye PDNN Nov05 / WebQTL + + + + + + + + + + + + + + + + + +

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+ +Eye M430v2 (November05) PDNN

Accession number: GN94

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Summary:

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+CAUTION: DO NOT USE THIS PDNN TRANSFORM of the HEIMED EYE Database. USE RMA INSTEAD. This April 2005 data freeze provides estimates of mRNA expression in adult eye from 50 lines of mice including C57BL/6J, DBA/2J, their F1 hybrids, and 47 BXD recombinant inbred strains. Data were generated at UTHSC. Samples were hybridized in small pools (n = 3) to Affymetrix M430 2.0 arrays. This particular data set was processed using the PDNN method of Zhang. To simplify comparison among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units. +
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About the cases used to generate this set of data:

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+We have used a set of BXD recombinant inbred strains generated by crossing C57BL/6J (B6 or B) with DBA/2J (D2 or D). The BXDs are particularly useful for systems genetics because both parental strains have been sequenced (8x coverage of B6 and 1.5x coverage of D). Physical maps in WebQTL incorporate approximately 2 million B vs D SNPs from Celera Genomics and from the Perlegen-NIEHS sequencing effort. BXD2 through BXD32 were bred by Benjamin A. Taylor starting in the late 1970s. BXD33 through 42 were bred by Taylor in the 1990s. These strains are available from The Jackson Laboratory. BXD43 through BXD99 were bred by Lu Lu, Jeremy Peirce, Lee M. Silver, and Robert W. Williams in the late 1990s and early 2000s using advanced intercross progeny (Peirce et al. 2004). Many of the 50 new BXD strains are available from Lu Lu and colleagues.
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All stock was obtained originally from The Jackson Laboratory between 1998 and 2003. Most BXD animals were born and housed at the University of Tennessee Health Science Center. Some cases were bred at the University of Memphis (Douglas Matthews) or the University of Alabama (John Mountz and Hui-Chen Hsu). +

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About the tissue used to generate this set of data:

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The INIA M430 brain Database (April05) consists of 105 Affymetrix 430A and 430B microarray pairs. Each pair was hybridized in sequence (A array first, B array second) with a pool of brain tissue (forebrain minus olfactory bulb, plus the entire midbrain) taken from three adult animals of closely matched age and the same sex. RNA was extracted at UTHSC by Lu Lu, Zhiping Jia, and Hongtao Zhai at UTHSC. + +
Tissue preparation protocol. Animal were killed by rapid cervical dislocation. Eyes were removed immediately and placed in RNAlater at room temperature. Usually six eyes from animals with a common sex, age, and strain were stored in a single tube. The body was sprayed lightly with 70% ethanol to wet the hair. the following standard approach was used to extract the brain: + +
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Using small surgical scissors make an incision under the skin on the dorsal side of the neck. Cut the skin overlying the skull close to the midsagittal plane towards the nose. Pull and reflect the skin to expose the entire dorsal skull. +
Slip the points of the scissors through into the cisterna magna just caudal to the cerebellum and gently enlarge this opening until is it possible to cut through the skull overlying the cerebellum. +
Cut rostrally through the skull along the midsagittal line almost all the way to the nasal opening, taking care not to damage the dorsal surface of the brain. +
Approximately midway along this incision, make a lateral cut. Repeat along the incision and peel back the resulting strips of skull. +
Using small forceps, free the olfactory bulbs rostrally and ventrally, taking care to retain their connection to the rest of the forebrain. +
Gently lift the brain from the base the skull starting from the olfactory bulbs, pulling the brain toward a nearly vertical position. Cut the optic and trigeminal nerves. Separate the brain from the spinal cord about 2 mm distal to the medulla. +
Spread the hemispheres of the forebrain gently with forceps and then cut from dorsal to ventral using a straight scalpel, separating the hemispheres from each other (but not from the cerebellum). Take care to retain both paraflocculi. +
+ +At this point the protocol divides. If tissue is to be saved for RNA extraction at a later time, the whole brain is placed directly in RNAlater (Ambion, Inc.) and treated per the manufacturer’s directions. Step 7 is still very important because RNAlater may not fully penetrate the forebrain if the lobes are not separated. If tissue is to be used for immediate RNA extraction, one lobe of the forebrain is removed for processing and the rest of the brain is stored in RNAlater.
+ +Dissecting and preparing forebrain and midbrain for RNA extraction +
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Remove the left or right hemisphere of the forebrain and midbrain (referred to here as the forebrain for simplicity), either fresh or preserved in RNAlater by cutting from the caudal border of the inferior colliculus on the dorsal side and extending the cut ventrally to the basis pedunculi and the pons (cut just rostral of the pons) on the ventral side. See steps 7 and 8 here +
Place tissue for RNA extraction in RNA STAT-60 (Tel-Test Inc.) and process per manufacturer’s instructions (in brief form below). +
Store RNA in 75% ethanol at –80 deg. C until use. +
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Total RNA was extracted with RNA STAT-60 (Tel-Test) according to the manufacturer’s instructions. Briefly we: +
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homogenize tissue samples in the RNA STAT-60 (1 ml/50 to 100 mg tissue) +
allowed the homogenate to stand for 5 min at room temperature +
added 0.2 ml of chloroform per 1 ml RNA STAT-60 +
shook the sample vigorously for 15 sec and let the sample sit at room temperature for 3 min +
centrifuged at 12,000 G for 15 min +
transfered the aqueous phase to a fresh tube +
added 0.5 ml of isopropanol per 1 ml RNA STAT-60 +
vortexed and allowed sample to stand at room temperature for 5-10 min +
centrifugeed at 12,000 G for 10-15 min +
removed the supernatant and washed the RNA pellet with 75% ethanol +
stored the pellet in 75% ethanol at -80 deg C until use +
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Sample Processing. Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center of Excellence, The University of Memphis, lead by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, samples were quality control checked for RNA purity using 260/280 ratios (samples had to be greater than 1.8, but the majority were 1.9 or higher). RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8, based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II RT (Invitrogen Inc.). The Enzo LIfe Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. At this point the cRNA was evaluated again using both the 260/280 ratio (values of 2.0 or above are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nt is required). Those samples that passed both QC steps (10% usually fail) were then sheared using a fragment buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No.900371). After fragmentation, samples were either stored at -80 deg. centrigrade until use or were immediately injected onto the array. + +
Replication and Sample Balance: Our goal is to obtain data for independent biological sample pools from at least one of sample from each sex for all BXD strains. We have not yet achieved this goal. Ten of 45 strains are still represented by single sex samples: BXD2 (F), BXD8 (F), BXD15 (F), BXD18 (F), BXD25 (F), BXD29 (F), BXD33 (M), BXD45 (F), BXD77 (M), and BXD90 (M). Eleven strains are represented by three independent samples with the following breakdown by sex: C57BL/6J (1F 2M), DBA/2J (2F 2M), B6D2F1 (2F 2M) + D2B6F1 (1F 1M), BXD6 (2F 1M), BXD13 (2F 1M), BXD14 (1F 2M), BXD28 (2F 1M), BXD34 (1F 2M), BXD36 (1F 2M), BXD38 (1F 2M), BXD42 (1F 2M). + +
Batch Structure: Before running the first batch of 30 pairs of array (dated Jan04), we ran four test samples (Nov03). The main batch of 30 includes the four test samples (four technical replicates). The Nov03 data was combined with the Jan04 data and was treated as a single batch that consists of one male and one female pool from C57BL/6J, DBA/2J, the B6D2F1 hybrid, 11 female BXD samples, and 11 male BXD samples. The second large batch was run February 2005 (Feb05) and consists of 71 pairs of arrays. Batch effects were corrected at the individual probe level as described below. + + +
The table below summarizes information on tubeID, group_type, strain, age, sex, original CEL filename, and source of mice. + +

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Id tube ID group type Strain age sex original CEL filename PDNN 2Z outlier RMA 2Z outlier scale factor background average present absent marginal AFFX-b-ActinMur(3'/5') AFFX-GapdhMur(3'/5') source
1 R2607E1 GDP BXD C57BL/6J 67 F R2605E.CEL 0.005 0.009 2.428 115.12 0.586 0.4 0.014 1.31 0.76 UTM RW
2 R0872E2 GDP BXD C57BL/6J 66 M R0872E.CEL 0.013 0.012 3.128 88.58 0.589 0.396 0.015 1.3 0.79 UTM RW
3 R2572E1 GDP BXD DBA/2J 65 M R2572E.CEL 0.041 0.051 2.406 79.07 0.555 0.429 0.016 1.37 0.79 UTM RW
4 R2601E1 GDP BXD B6D2F1 73 F R2601E.CEL 0.003 0.004 2.545 91.96 0.589 0.396 0.015 1.44 0.78 UTM RW
5 R2602E1 GDP BXD B6D2F1 73 M R2602E.CEL 0.001 0.004 2.599 84.44 0.597 0.388 0.015 1.37 0.78 UTM RW
6 R2600E1 GDP BXD D2B6F1 72 F R2600E.CEL 0.003 0.008 2.47 94.75 0.581 0.402 0.017 1.41 0.78 UTM RW
7 R2604E1 GDP BXD D2B6F1 69 M R2604E.CEL 0.003 0.007 2.657 89.63 0.594 0.392 0.015 1.28 0.79 UTM RW
8 R2597E1 BXD BXD2 61 M R2597E.CEL 0.003 0.007 2.374 93.56 0.603 0.383 0.015 1.34 0.77 Glenn
9 R2591E1 BXD BXD5 60 F R2591E.CEL 0.051 0.009 1.7 136.48 0.585 0.4 0.015 1.33 0.78 Glenn
10 R2570E1 BXD BXD6 65 F R2570E.CEL 0.002 0.006 1.987 86.73 0.585 0.4 0.015 1.46 0.76 UTM RW
11 R2538E1 BXD BXD8 77 F R2538E.CEL 0.037 0.028 1.905 101.98 0.612 0.373 0.015 1.52 0.79 UTM RW
12 R2569E1 BXD BXD9 67 M R2569E.CEL 0.014 0.027 1.753 87.36 0.551 0.434 0.015 2.82 3.14 UTM RW
13 R2581E1 BXD BXD11 65 F R2581E.CEL 0.006 0.012 1.941 88.55 0.621 0.364 0.016 1.55 0.81 UTM RW
14 R2543E1 BXD BXD12 63 M R2543E.CEL 0.036 0.007 1.605 117.69 0.586 0.399 0.016 1.43 0.77 UTM RW
15 R2586E1 BXD BXD13 60 F R2586E.CEL 0.020 0.035 2.006 73.61 0.564 0.42 0.016 2.85 3.81 Glenn
16 R2557E1 BXD BXD14 60 F R2557E.CEL 0.014 0.017 1.83 98.76 0.625 0.361 0.014 1.31 0.78 Glenn
17 R2567E1 BXD BXD16 60 M R2567E.CEL 0.016 0.025 2.239 82.35 0.567 0.416 0.017 1.37 0.75 Glenn
18 R2559E1 BXD BXD18 59 M R2559E.CEL 0.035 0.006 1.654 103.68 0.608 0.377 0.015 1.27 0.78 Glenn
19 R2560E1 BXD BXD19 60 F R2560E.CEL 0.026 0.007 1.792 98.33 0.609 0.375 0.016 1.35 0.8 Glenn
20 R2584E1 BXD BXD20 59 F R2584E.CEL 0.003 0.007 2.07 83.82 0.593 0.391 0.016 1.4 0.76 Glenn
21 R2541E2 BXD BXD21 61 M R2541E2.CEL 0.049 0.036 2.625 125.08 0.56 0.424 0.015 1.29 0.78 UTM RW
22 R2553E1 BXD BXD22 58 F R2553E.CEL 0.003 0.005 1.952 111.3 0.599 0.385 0.015 1.28 0.76 Glenn
23 R2558E1 BXD BXD23 60 F R2558E-2.CEL 0.013 0.015 1.908 114.53 0.599 0.388 0.014 1.2 0.82 Glenn
24 R2589E2 BXD BXD24 59 M R2589E2.CEL 0.098 0.098 2.606 112.19 0.575 0.409 0.016 1.24 0.8 Glenn
25 R2573E1 BXD BXD25 67 F R2573E-2.CEL 0.009 0.018 3.153 71.88 0.579 0.407 0.014 1.77 0.97 UAB
26 R2562E1 BXD BXD28 60 F R2562E.CEL 0.003 0.005 1.649 116.35 0.599 0.384 0.017 1.37 0.79 Glenn
27 R2561E1 BXD BXD29 60 F R2561E.CEL 0.019 0.029 1.952 93.32 0.583 0.402 0.015 2.19 1 Glenn
28 R2598E1 BXD BXD31 61 M R2598E.CEL 0.003 0.006 1.989 106.48 0.609 0.376 0.015 1.27 0.78 UTM RW
29 R2563E1 BXD BXD32 63 F R2563E.CEL 0.008 0.011 1.547 101.52 0.619 0.367 0.014 1.5 0.8 UTM RW
30 R2542E1 BXD BXD33 67 F R2542E.CEL 0.010 0.016 2.128 97.08 0.565 0.418 0.016 1.91 0.93 UTM RW
31 R2585E1 BXD BXD34 60 M R2585E.CEL 0.007 0.014 2.64 75.13 0.583 0.4 0.017 1.25 0.77 Glenn
32 R2532E1 BXD BXD38 62 M R2532E.CEL 0.002 0.003 2.038 93.65 0.598 0.387 0.015 1.37 0.8 UTM RW
33 R2574E1 BXD BXD39 70 F R2574E.CEL 0.001 0.004 1.981 90.64 0.612 0.373 0.015 1.39 0.78 UTM RW
34 R2590E1 BXD BXD40 60 M R2590E.CEL 0.004 0.007 2.708 77.3 0.591 0.393 0.015 1.4 0.77 Glenn
35 R2596E1 BXD BXD42 59 M R2596E.CEL 0.013 0.017 2.632 108.46 0.59 0.396 0.015 1.24 0.8 Glenn
36 R2605E1 BXD BXD43 79 M R2607E.CEL 0.003 0.006 1.817 131.22 0.605 0.382 0.013 1.32 0.8 UTM RW
37 R2594E1 BXD BXD44 63 F R2594E.CEL 0.004 0.009 1.766 117.33 0.598 0.388 0.014 1.35 0.85 UTM RW
38 R2592E1 BXD BXD45 62 M R2592E.CEL 0.002 0.004 1.85 106.16 0.601 0.386 0.013 1.43 0.85 UTM RW
39 R2606E1 BXD BXD48 78 M R2606E.CEL 0.003 0.010 2.556 106.16 0.589 0.397 0.014 1.35 0.83 UTM RW
40 R2603E1 BXD BXD51 66 F R2603E.CEL 0.003 0.009 2.488 115.16 0.577 0.408 0.015 1.24 0.79 UTM RW
41 R2534E2 BXD BXD61 70 F R2534E2.CEL 0.030 0.028 2.473 117.76 0.579 0.406 0.015 1.42 0.79 UTM RW
42 R2611E1 BXD BXD64 68 M R2611E.CEL 0.013 0.022 2.292 91.99 0.58 0.405 0.015 1.57 1.06 UTM RW
43 R2583E1 BXD BXD65 60 M R2583E.CEL 0.005 0.010 2.492 70.43 0.569 0.415 0.016 1.67 1.01 UTM RW
44 R2536E2 BXD BXD66 64 F R2536E2.CEL 0.039 0.065 2.74 108.62 0.561 0.423 0.017 1.28 0.79 UTM RW
45 R2551E1 BXD BXD68 67 F R2551E.CEL 0.037 0.039 2.493 92.38 0.543 0.441 0.016 2.91 1.55 UTM RW
46 R2593E1 BXD BXD69 59 F R2593E.CEL 0.008 0.013 1.672 127.6 0.592 0.395 0.013 1.47 0.92 UTM RW
47 R2537E2 BXD BXD70 59 M R2537E2.CEL 0.046 0.044 2.93 98.66 0.58 0.405 0.016 1.29 0.75 UTM RW
48 R2565E1 BXD BXD75 61 F R2565E.CEL 0.009 0.017 1.79 101.68 0.58 0.405 0.015 2.31 3.47 UTM RW
49 R2579E1 BXD BXD80 65 F R2579E.CEL 0.005 0.010 2.419 72.13 0.592 0.394 0.015 1.73 0.82 UTM RW
50 R2540E1 BXD BXD87 63 M R2540E.CEL 0.013 0.016 2.333 93.15 0.611 0.374 0.014 1.22 0.81 UTM RW
51 R2545E1 BXD BXD89 67 M R2546E.CEL 0.046 0.046 1.667 104.76 0.562 0.423 0.015 3.6 9.84 UTM RW
52 R2578E2 BXD BXD90 61 F R2578E2.CEL 0.033 0.034 2.785 92.27 0.586 0.398 0.016 1.52 0.77 UTM RW
53 R2554E1 BXD BXD96 67 M R2554E.CEL 0.004 0.004 2.177 93.02 0.602 0.383 0.015 1.46 0.77 UTM RW
54 R2577E1 BXD BXD97 55 M R2577E.CEL 0.019 0.016 2.07 76.58 0.595 0.391 0.014 1.87 1.29 UTM RW
55 R2595E1 GDP 129S1/SvImJ 59 F R2595E.CEL 0.017 0.021 1.792 115.39 0.61 0.375 0.015 1.46 0.77 UTM RW
56 R2533E1 GDP 129S1/SvImJ 60 M R2533E.CEL 0.021 0.013 2.107 93.55 0.579 0.405 0.016 1.37 0.78 UTM RW
57 R2546E1 GDP A/J 66 F R2545E.CEL 0.018 0.014 1.989 95.59 0.586 0.397 0.017 1.47 0.78 UTM RW
58 R0754E2 GDP A/J 60 M R0754E.CEL 0.014 0.016 2.718 85.63 0.598 0.387 0.015 1.36 0.76 JAX
59 R1676E1 GDP BALB/cByJ 83 F R1676E.CEL 0.042 0.041 2.685 98.37 0.589 0.396 0.015 1.46 0.74 JAX
60 R1672E1 GDP BALB/cByJ 83 M R1672E.CEL 0.022 0.022 2.216 110.52 0.599 0.386 0.015 1.26 0.8 JAX
61 R1700E1 GDP C3H/HeJ 83 F R1700E.CEL 0.090 0.092 2.978 68.77 0.608 0.379 0.014 1.48 0.78 UTM RW
62 R1704E1 GDP C3H/HeJ 83 M R1704E.CEL 0.086 0.089 2.581 88.29 0.601 0.386 0.013 1.38 0.84 UTM RW
63 R2564E1 GDP CAST/Ei 64 F R2564E.CEL 0.078 0.064 1.937 88.89 0.585 0.399 0.016 1.6 0.77 JAX
64 R2580E1 GDP CAST/Ei 64 M R2580E.CEL 0.076 0.067 2.089 94.64 0.582 0.401 0.017 1.4 0.76 JAX
65 R2636E1 GDP KK/HIJ 64 F R2636E.CEL 0.023 0.026 2.61 93.1 0.589 0.395 0.015 1.39 0.76 UTM RW
66 R2637E1 GDP KK/HIJ 64 M R2637E.CEL 0.039 0.020 2.189 102.78 0.594 0.39 0.015 1.3 0.79 UTM RW
67 R0999E1 GDP LG/J 57 F R0999E.CEL 0.012 0.012 2.448 82.09 0.594 0.391 0.015 1.38 0.79 UTM RW
68 R1004E1 GDP LG/J 65 M R1004E.CEL 0.013 0.015 2.438 91.71 0.587 0.398 0.015 1.38 0.79 UTM RW
69 R1688E1 GDP NOD/LtJ 66 F R1688E.CEL 0.017 0.019 2.664 97.65 0.586 0.399 0.015 1.26 0.8 JAX
70 R2566E1 GDP NOD/LtJ 76 M R2566E-2.CEL 0.019 0.025 3.031 69.44 0.598 0.388 0.015 1.38 0.75 UTM RW
71 R2550E1 GDP NZO/HlLtJ 96 M R2550E.CEL 0.023 0.015 1.794 87.16 0.607 0.378 0.015 1.52 0.82 JAX
72 R2535E1 GDP NZO/HlLtJ 62 F R2535E.CEL 0.046 0.025 1.893 85.67 0.604 0.382 0.014 1.41 0.85 JAX
73 R2634E1 GDP PWD/PhJ 62 F R2635E.CEL 0.077 0.069 3.292 89.8 0.559 0.425 0.016 1.57 0.81 JAX
74 R2635E1 GDP PWD/PhJ 62 M R2634E.CEL 0.088 0.081 3.722 80.05 0.542 0.441 0.017 1.53 0.85 JAX
75 R2544E1 GDP PWK/PhJ 63 F R2544E.CEL 0.106 0.100 2.196 107.51 0.549 0.435 0.017 1.36 0.82 JAX
76 R2549E1 GDP PWK/PhJ 83 M R2549E.CEL 0.065 0.048 2.275 83.8 0.573 0.412 0.015 1.57 0.83 JAX
77 R2368E1 GDP WSB/EiJ 67 F R2368E.CEL 0.025 0.028 2.567 85.7 0.595 0.391 0.014 1.29 0.74 UTM RW
78 R2547E1 GDP WSB/EiJ 67 M R2547E.CEL 0.032 0.021 2.135 90.04 0.582 0.401 0.016 1.32 0.77 UTM RW

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About the array platfrom :

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Affymetrix Mouse Genome 430v2: The 430A and B array pairs collectively consist of 992936 25-nucleotide probes that estimate the expression of approximately 39,000 transcripts (many are essentially duplicates). The array sequences were selected late in 2002 using Unigene Build 107. The arrays nominally contain the same probe sequence as the 430 2.0 series. However, we have found that roughy 75000 probes differ between those on A and B arrays and those on the 430 2.0.
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About data processing:

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Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of 91 pixel values per cell. +
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Step 1: We added an offset of 1.0 unit to each cell signal to ensure that all values could be logged without generating negative values. We then computed the log base 2 of each cell. + +
Step 2: We performed a quantile normalization of the log base 2 values for the total set of 105 arrays (processed as two batches) using the same initial steps used by the RMA transform. + +
Step 3: We computed the Z scores for each cell value. + +
Step 4: We multiplied all Z scores by 2. + +
Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference. + +
Step 6: We eliminated much of the systematic technical variance introduced by the two batches (n = 34 and n = 71 array pairs) at the probe level. To do this we calculated the ratio of each batch mean to the mean of both batches and used this as a single multiplicative probe-specific batch correction factor. The consequence of this simple correction is that the mean probe signal value for each batch is the same. + +
Step 7a: The 430A and 430B arrays include a set of 100 shared probe sets (a total of 2200 probes) that have identical sequences. These probes and probe sets provide a way to calibrate expression of the 430A and 430B arrays to a common scale. To bring the two arrays into alignment, we regressed Z scores of the common set of probes to obtain a linear regression correction to rescale the 430B arrays to the 430A array. In our case this involved multiplying all 430B Z scores by the slope of the regression and adding or subtracting a small offset. The result of this step is that the mean of the 430A expression is fixed at a value of 8, whereas that of the 430B chip is typically reduced to 7. The average of the merged 430A and 430B array data set is approximately 7.5. + +
Step 7b: We recentered the merged 430A and 430B data sets to a mean of 8 and a standard deviation of 2. This involved reapplying Steps 3 through 5. + +
Step 8: Finally, we computed the arithmetic mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples. Note, that we have not (yet) corrected for variance introduced by differences in sex, age, source of animals, or any interaction terms. We have not corrected for background beyond the background correction implemented by Affymetrix in generating the CEL file. We eventually hope to add statistical controls and adjustments for some of these variables. + +
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Data source acknowledgment:
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+Support for acquisition of microarray data were generously provided by the NIAAA and its INIA grant program to RWW, Thomas Sutter, and Daniel Goldowitz (U01AA013515, U01AA013499-03S1, U01AA013488, U01AA013503-03S1). Support for the continued development of the GeneNetwork and WebQTL was provided by a NIMH Human Brain Project grant (P20MH062009). All arrays were processed at the University of Memphis by Thomas Sutter and colleagues with support of the INIA Bioanalytical Core. +
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Information about this text file:
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This text file originally generated by RWW, YHQ, and EJC, Oct 2004. Updated by RWW, Nov 5, 2004; April 7, 2005; RNA/tissue preparation protocol updatedby JLP, Sept 2, 2005; Sept 26, 2005. +
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