Question: Print Differentially Expressed Exons From Dexseq Results
0
gravatar for justinkablan225
3 months ago by
justinkablan2250 wrote:
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.
dexseq rna-seq • 122 views
ADD COMMENTlink modified 3 months ago by Alejandro Reyes1.7k • written 3 months ago by justinkablan2250
Answer: Print Differentially Expressed Exons From Dexseq Results
2
gravatar for Alejandro Reyes
3 months ago by
Alejandro Reyes1.7k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.7k wrote:

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

ADD COMMENTlink modified 3 months ago • written 3 months ago by Alejandro Reyes1.7k
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