From b2feda451ccfbeaed02dce9088d6dd228cf15861 Mon Sep 17 00:00:00 2001 From: Bonface Date: Tue, 13 Feb 2024 23:52:26 -0600 Subject: Update dataset RTF Files. --- .../Illum_retina_bxd_rankinv0410/experiment-design.rtf | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 general/datasets/Illum_retina_bxd_rankinv0410/experiment-design.rtf (limited to 'general/datasets/Illum_retina_bxd_rankinv0410/experiment-design.rtf') diff --git a/general/datasets/Illum_retina_bxd_rankinv0410/experiment-design.rtf b/general/datasets/Illum_retina_bxd_rankinv0410/experiment-design.rtf new file mode 100644 index 0000000..4fff707 --- /dev/null +++ b/general/datasets/Illum_retina_bxd_rankinv0410/experiment-design.rtf @@ -0,0 +1,12 @@ +

Expression profiling by array

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We used pooled RNA samples of retinas, usually two independent pools--two male, two female pool--for most lines of mice.

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All normalization was performed by William E. Orr in the HEI Vision Core Facility

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  1. Computed the log base 2 of each raw signal value
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  2. Calculated the mean and standard Deviation of each Mouse WG-6 v2.0 array
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  3. Normalized each array using the formula, 2 (z-score of log2 [intensity]) The result is to produce arrays that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
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  4. computed the mean of the values for the set of microarrays for each strain. Technical replicates were averaged before computing the mean for independent biological samples.
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