From e34e7da50fc0ff5ed41e8bdaf2b1d41c9e9cf534 Mon Sep 17 00:00:00 2001 From: Bonface Date: Thu, 15 Feb 2024 06:09:54 -0600 Subject: Update dataset RTF Files. --- .../UMUTAffyExon_0209_RMA/acknowledgment.rtf | 1 - general/datasets/UMUTAffyExon_0209_RMA/cases.rtf | 1182 -------------------- .../datasets/UMUTAffyExon_0209_RMA/processing.rtf | 9 - general/datasets/UMUTAffyExon_0209_RMA/summary.rtf | 3 - 4 files changed, 1195 deletions(-) delete mode 100644 general/datasets/UMUTAffyExon_0209_RMA/acknowledgment.rtf delete mode 100644 general/datasets/UMUTAffyExon_0209_RMA/cases.rtf delete mode 100644 general/datasets/UMUTAffyExon_0209_RMA/processing.rtf delete mode 100644 general/datasets/UMUTAffyExon_0209_RMA/summary.rtf (limited to 'general/datasets/UMUTAffyExon_0209_RMA') diff --git a/general/datasets/UMUTAffyExon_0209_RMA/acknowledgment.rtf b/general/datasets/UMUTAffyExon_0209_RMA/acknowledgment.rtf deleted file mode 100644 index 9f0655d..0000000 --- a/general/datasets/UMUTAffyExon_0209_RMA/acknowledgment.rtf +++ /dev/null @@ -1 +0,0 @@ -

We thank Affymetrix Inc. for their generous support of this project and array data set.

diff --git a/general/datasets/UMUTAffyExon_0209_RMA/cases.rtf b/general/datasets/UMUTAffyExon_0209_RMA/cases.rtf deleted file mode 100644 index 35ae421..0000000 --- a/general/datasets/UMUTAffyExon_0209_RMA/cases.rtf +++ /dev/null @@ -1,1182 +0,0 @@ - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
IndexOriginal CELTube IDStrainAgeSexSource
1JR3551H.CELjr3551hC57BL/6J60FUTM RW
2JR3552H.CELjr3552hreC57BL/6J60FUTM RW
3R0572H.CELr0572hC57BL/6J69F 
4R2137H.CELr2137hC57BL/6J55FJAX
5R3552H.CELr3552hC57BL/6J60FGlenn
6JR3549H.CELjr3549hC57BL/6J60MUTM RW
7JR3550H.CELjr3550hreC57BL/6J60MUTM RW
8R0574H.CELr0574hC57BL/6J69M 
9R2136H.CELr2136hC57BL/6J55MJAX
10R3549H.CELr3549hC57BL/6J60MGlenn
11JR3557H.CELjr3557hDBA/2J60FUTM RW
12JR3558H.CELjr3558hreDBA/2J60FUTM RW
13R3558H.CELr3558hDBA/2J60FGlenn
14JR3555H.CELjr3555hDBA/2J60MUTM RW
15JR3556H.CELjr3556hDBA/2J60MUTM RW
16R3555H.CELr3555hDBA/2J60MGlenn
17R3497H.CELr3497hB6D2F158FGlenn
18R3500H.CELr3500hB6D2F158MGlenn
19R1374H.CELr1374hD2B6F158FUTM RW
20R1382H.CELr1382hD2B6F159MUTM RW
21R3532H.CELr3532h129S1/SvImJ60FGlenn
22R3512H.CELr3512h129S1/SvImJ59MGlenn
23R3520H.CELr3520hA/J59FGlenn
24R3523H.CELr3523hA/J59MGlenn
25R3514H.CELr3514hAKR/J59FGlenn
26R3515H.CELr3515hAKR/J59MGlenn
27R3508H.CELr3508hBALB/cByJ59FGlenn
28R3505H.CELr3505hBALB/cByJ59MGlenn
29R3524H.CELr3524hBTBR T+ tf/J60FGlenn
30R3509H.CELr3509hBTBR T+ tf/J60MGlenn
31R1542H.CELr1542hBXD159FGlenn
32R1520H.CELr1520hBXD256FGlenn
33R1694H.CELr1694hBXD558MGlenn
34R3454H.CELr3454hBXD658MGlenn
35R3457H.CELr3457hBXD861FGlenn
36R3455H.CELr3455hBXD960MGlenn
37R3462H.CELr3462hBXD1159MGlenn
38R3464H.CELr3464hBXD1259FGlenn
39R2315H.CELr2315hBXD1384MUTM RW
40R3480H.CELr3480hBXD1460FGlenn
41R3478H.CELr3478hBXD1560MGlenn
42R3482H.CELr3482hBXD1659FGlenn
43R3488H.CELr3488hBXD1859MGlenn
44R3471H.CELr3471hBXD1960MGlenn
45R2506H.CELr2506hBXD2060MGlenn
46R3490H.CELr3490hBXD2160FGlenn
47R3492H.CELr3492hBXD2260FGlenn
48R3486H.CELr3486hBXD2360FGlenn
49R1547H.CELr1547hBXD2459MGlenn
50R2892H.CELr2892hBXD2567FUTM RW
51R3485H.CELr3485hBXD2760MGlenn
52R3477H.CELr3477hBXD2860FGlenn
53R3475H.CELr3475hBXD2960FGlenn
54R3456H.CELr3456hBXD3160MGlenn
55R3570H.CELr3570hBXD3266F 
56R3571H.CELr3571hBXD3258M 
57R3467H.CELr3467hBXD3359MGlenn
58R3466H.CELr3466hBXD3460FGlenn
59R3463H.CELr3463hBXD3661FGlenn
60R3458H.CELr3458hBXD3855MGlenn
61JR4433H.CELjr4433saBXD3963FUTM RW
62R1535H.CELr1535hBXD3960FGlenn
63R3459H.CELr3459hBXD4060MGlenn
64R1541H.CELr1541hBXD4258FGlenn
65R1279H.CELr1279hBXD4357MUTM RW
66R1472H.CELr1472hBXD4565MUTM RW
67R1586H.CELr1586hBXD4859FUTM RW
68R2936H.CELr2936hBXD5061FUTM RW
69R1313H.CELr1313hBXD5162MUTM RW
70JR2680H.CELjr2680hBXD5565MUTM RW
71R1340H.CELr1340hBXD6064FUTM RW
72R1856H.CELr1856hBXD6194MUTM RW
73R1317H.CELr1317hBXD6259FUTM RW
74R1945H.CELr1945hBXD63107FUTM RW
75R2615H.CELr2615hBXD6468FUTM RW
76R3567H.CELr3567hBXD6560FUTRW
77R1949H.CELr1949hBXD6696MUTM RW
78R2060H.CELr2060hBXD6754FUTM RW
79R2902H.CELr2902hBXD6857MUTM RW
80R1466H.CELr1466hBXD6959FUTM RW
81R2063H.CELr2063hBXD7055MUTM RW
82R1269H.CELr1269hBXD7372MUTM RW
83JR2316H.CELjr2316hreBXD74193MUTM RW
84R1871H.CELr1871hBXD7561FUTM RW
85JR1948H.CELjr1948hBXD7681FUTM RW
86R1427H.CELr1427hBXD7761MUTM RW
87JR4434H.CELjr4434sareBXD7963FUTM RW
88R3568H.CELr3568hBXD8066MUTRW
89R2959H.CELr2959hBXD8358FUTM RW
90R2898H.CELr2898hBXD8467MUTM RW
91R3566H.CELr3566hBXD8565MUTRW
92R1556H.CELr1556hBXD8657FUTM RW
93R1710H.CELr1710hBXD8784MUTM RW
94JR4079H.CELjr4079hreBXD8963MUTM RW
95R2058H.CELr2058hBXD9061FUTM RW
96R1284H.CELr1284hBXD9258MUTM RW
97JR2057H.CELjr2057hBXD9392FUTM RW
98JR2313H.CELjr2313h-reBXD9459FUTM RW
99R1915H.CELr1915hBXD9665FUTM RW
100R2648H.CELr2648hBXD9774FUTM RW
101R1942H.CELr1942hBXD9862FUTM RW
102R1369H.CELr1369hBXD9976MUMemphis
103R2889H.CELr2889hBXSB/MpJ61FGlenn
104R2887H.CELr2887hBXSB/MpJ61MGlenn
105R3501H.CELr3501hC3H/HeJ60FGlenn
106R3504H.CELr3504hC3H/HeJ60MGlenn
107R3564H.CELr3564hCAST/EiJ57FGlenn
108R3565H.CELr3565hCAST/EiJ61MGlenn
109R3493H.CELr3493hFVB/NJ60FGlenn
110R3496H.CELr3496hFVB/NJ60MGlenn
111JR1683H.CELjr1683hKK/HlJ72FUTM RW
112JR3542H.CELjr3542hreKK/HlJ61MUTM RW
113JR2046H.CELjr2046hreLG/J63FUTM RW
114JR2047H.CELjr2047hLG/J63MUTM RW
115R3541H.CELr3541hMOLF/EiJ60FGlenn
116R3553H.CELr3553hMOLF/EiJ60MGlenn
117R3516H.CELr3516hNOD/LtJ58FGlenn
118R3519H.CELr3519hNOD/LtJ58MGlenn
119R3554H.CELr3554hNZB/BlNJ61FGlenn
120R3513H.CELr3513hNZB/BlNJ58MGlenn
121R3539H.CELr3539hNZO/HlLtJ60FGlenn
122R3536H.CELr3536hNZO/HlLtJ60MGlenn
123R3540H.CELr3540hNZW/LacJ65FGlenn
124R3535H.CELr3535hNZW/LacJ60MGlenn
125R3527H.CELr3527hPWD/PhJ60FGlenn
126R3526H.CELr3526hPWD/PhJ60MGlenn
127R3531H.CELr3531hPWK/PhJ60MGlenn
128R3561H.CELr3561hWSB/EiJ60FGlenn
129R3525H.CELr3525hWSB/EiJ60MGlenn
-
diff --git a/general/datasets/UMUTAffyExon_0209_RMA/processing.rtf b/general/datasets/UMUTAffyExon_0209_RMA/processing.rtf deleted file mode 100644 index 6e4dc8e..0000000 --- a/general/datasets/UMUTAffyExon_0209_RMA/processing.rtf +++ /dev/null @@ -1,9 +0,0 @@ -

The following steps were applied to refine the data by M. Jagalur in RWW lab:

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  1. Strain correction: In this step the strong probe level cis-QTLs were identified and using an expectation maximization (EM)-like method, the genotypes of each marker was re-assigned. This set of reassigned markers was compared to existing list genotypes of BXD strains and the maximal match was identified as the correct strain.
    2. -
  2. Sex correction: In this step probes that are highly correlated to sex were identified and using an EM-like method we detected and corrected the sex of single array data sets.
    3. -
  3. Data exclusion criteria: In this step individual arrays were evaluated. Arrays were systematically excluded from the data set (drop one out) and the number of cis-QTLs was recomputed. If excluding an array resulted in s significantly higher number of cis-QTLs then that array was considered to be of poor quality and was excluded from the final data set This step was repeated across all arrays in multiple cycles until there was no improvement in number of cis-QTLs.
    4. -
  4. Tissue correction: In this step probes that are highly correlated to tissue type were identified and EM-like method was used to identify correct tissue.
    5. -
  5. Noise Removal: A noise component was calculated using the expression of "unhybridized"probes (those with the lowest signal) and was removed from the data.
    6. -
diff --git a/general/datasets/UMUTAffyExon_0209_RMA/summary.rtf b/general/datasets/UMUTAffyExon_0209_RMA/summary.rtf deleted file mode 100644 index a1fe16a..0000000 --- a/general/datasets/UMUTAffyExon_0209_RMA/summary.rtf +++ /dev/null @@ -1,3 +0,0 @@ -

Data generated by RW Williams, Lu Lu, Manjunatha Jagalur, and David Kulp. All arrays run at the VA Medical Center, Memphis, by Yan Jiao.

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Data entered by Arthur Centeno and Manju Jagalur, Feb 27, 2009. This data set modified data for two BXD strains. Data were added for BXD79 that had been incorrectly included as a striatum sample (this data set was therefore deleted from the Exon 1.0ST striatum data set). We also changed data for BXD39. As expected, this addition and correction improved QTL mapping values. For example, for Kcnj9 probe set 4519178 the LRS values increased from 103.3 in the Aug08 data to 115.7 for these Feb09 data. Rob is concerned about the high error term of BXD39.

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