table of fold change P value and FDR for comparison of groups
Sep 5, 2018 10:34 AM(1816 views)
I have datasets with many response variables (~15K) and many samples (~7K). I have clustered the samples based on prior knowledge into 10 clusters, and need to define the variables that are characteristic for each. I want to generate a table/matrix that lists all the variables vs the clusters, with the fold change (ratio) in mean response values (each cluster vs all other samples together) with P values (either corrected or not) and FDR if possible.
Hoping there is a simple way to generate this. ANOVA or negative binomial options would be helpful.
My experience in such cases was in virology when the useful information was a doubling but the response was titer. So a transformation could make the response more meaningful transforming as Ln( titer ) / Ln( 2 ). (That is effectively the logarithm base 2.) You can do this transformation with a column formula without the need for a separate script.