Hello,
I'm trying to do some differential expressed exons analysis with DEXSeq package. I got DEXSeq results by :

> dxr1 = DEXSeqResults( dxdEFC, padj=0.1 )

Then, I'm looking for print only Up-regulate or Down-regulate exons significantly expressed. 

Therefore, I done :

> write.table(dxr1, "DEXSeq_results" , sep="\t", col.names=T, row.names = T) 

This script gave me all genes and exons in a single file within more than 60.000 rows what is very difficult to open and then difficult to sort by padj or FDR.

I think that someone can help me here to resolve that, I will be very grateful. 

Best regards.

Hi justinkablan225,

If you want to subset the data for those exons that are significant according to DEXSeq, you can subset as you would subset any data frame:

data(pasillaDEXSeqDataSet, package="pasilla")
dxr <- DEXSeq( dxd )
dxr[which( dxr$padj < 0.1 ),]

Alejandro