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Significance of found differences between samples were corrected for the design effect caused by weights.
Background and input variation between samples were corrected using signal intensities for negative control pixel noise and actin band intensities, respectively.
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Empirical Bayes moderated P-values for contrasting and comparing expression between all samples were corrected for multiple testing by the Strimmer method as implemented in the R package fdrtool [ 35].
All measurements in the samples were corrected for extraction efficiency.
Cy5- and Cy3-derived intensity data from the direct comparisons between the test sample and reference sample were corrected for intensity-dependent dye biases using a Lowess function implemented in the R package (The R Project for Statistical Computing [http://www.r-project.org]).org]
To compare expression level of a gene between different tissues studied, the mean Ct of each sample was corrected by this obtained for RPL19.
Each sample was corrected for background fluorescence.
To account for variations in mRNA extraction and reverse transcription reaction between samples, mRNA levels were corrected relative to ribosomal 18S rRNA levels.
Sample signals were corrected using this mean background signal.
To account for variations in mRNA extraction and reverse transcription reaction between samples, probe mRNA levels were corrected relative to Tata Binding Protein (TBP).
H4 samples with SO were corrected for SO fluorescence.
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