Question: How to return probelist,FC and p-value column by putting a p-value threshold in Limma
0
gravatar for Agaz Hussain Wani
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

ADD COMMENTlink 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
gravatar for Gordon Smyth
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.

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Gordon Smyth39k

Thanks for your answer.

ADD REPLYlink written 4.4 years ago by Agaz Hussain Wani260

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.

ADD REPLYlink written 4.4 years ago by Agaz Hussain Wani260

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.

ADD REPLYlink written 4.4 years ago by Aaron Lun25k
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