Question: How to return probelist,FC and p-value column by putting a p-value threshold in Limma
0
4.4 years ago by
India
Agaz Hussain Wani260 wrote:

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

modified 4.4 years ago by Gordon Smyth39k • written 4.4 years ago by Agaz Hussain Wani260
Answer: How to return probelist,FC and p-value column by putting a p-value threshold in
1
4.4 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

Yes, the topTable() function does this. For example

topTable(fit2, coef=2, n=Inf, p=0.01, adjust.method="none")

However I would strongly suggest that you consider using a multiple testing adjustment as well. Benjami-Hochberg is the default.

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.