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Hi,
I am using limma package to perform differential expression of Illumina data. I am wondering if i can get columns of probelist, foldchange and p-value by putting a threshold of say p-value <0.01. I can get probelist by using
sigGene <- probeList[ fit2$p.value[,2] < 0.01]
which returns the probelist only, however i am interested to get all the three columns mentioned above where the p-values is of my interest. Can i get this by using limma. Thanks
Thanks for your answer.
Is there something to set the value for number of studies to search in for significant gene. Say i have 12 studies with two treatment conditions, can i find a gene which is significant at-least in four studies or so depending on the p-value.
There's nothing off the shelf to do this, and it's not trivial to implement. The multiple testing situation is even more complicated here, as you'd have to account for multiple studies as well as multiple genes.