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Old 04-23-2014, 01:00 PM   #1
fgajardoe
Junior Member
 
Location: Santiago

Join Date: Apr 2013
Posts: 7
Default sum 1 to whole count matrix in differential expression analysis. its ok?

Hello everybody.

In our laboratory we are analyzing RNAseq data to do a differential expression analysis. Now we are using DESeq and we want to select the most differentially expressed genes using just fold change value. The RNAseq experiment has no replicates, so i dont care about statistics. it is just a descriptive study.

The problem is that we cannot sort the list because of "Inf" and "-Inf" fold change values. We are thinking to sum 1 to the whole count matrix to avoid the zero counts problem. Is this a good idea? Is there some inconvenients?

Thanks in advance

Last edited by fgajardoe; 04-23-2014 at 01:13 PM.
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Old 04-23-2014, 01:27 PM   #2
dpryan
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Location: Freiburg, Germany

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You might have a little better luck with GFold, or with simply setting a minimum read threshold in both samples.
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