DESeq2 for Differential gene expression

Question

[sana777munquad]

Hi

Currently I am working on differential gene expression and using DESeq2 package but during execution I got error that expression values should be integer and my expression values in float form. How can I resolve this issue?

Answer 1

[Arindam Ghosh]

Which tool did you use to generate expression values? I usually use FeatureCounts and I have not experienced float expression value yet. Also please check if the expression values are raw counts or has been pre-normalised. Float expression values are possible after normalisation. DESeq2 requires non-normalised data.

Answer 2

[Shalu Jhanwar]

Are you using RSEM Salmon, kallisto etc for quantification of expression counts? If yes, you can directly import counts in DEseq2 object using tximport package. For e.g. counts from RSEM can be imported by setting type to rsem, and txIn and txOut to FALSE. Have a look at https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html.

Hope this helps!