Question: Real-valued HTseq count to DESeq2
gravatar for english.server
7 months ago by
english.server160 wrote:


In order to input non-integer values to DESEQ2, the thread at

suggests that one rounds the values. I am not much familiar with RNA-seq analysis pipelines but I suppose HT-seq count should give integers as row counts or as I saw somewhere at real values as count estimates. I am not sure whether it is possible to round data available at

and then pass it to DESEQ2, ie is the thread at bioconductor website also applicable to this sort of data? The dataset is gene expression RNAseq - HTSeq - Counts from TCGA Uterine Carcinosarcoma (UCS).

Thank you

deseq2 htseq • 280 views
ADD COMMENTlink modified 7 months ago by Kevin Blighe53k • written 7 months ago by english.server160
gravatar for Kevin Blighe
7 months ago by
Kevin Blighe53k
Kevin Blighe53k wrote:

I presume that it was you who just up-voted my other [related] thread this morning: A: Normalisation of RNAseq data from UCSC Xena Browser ?

In that thread, I also recommend to round the counts to 0 decimal places, i.e., round them to integer counts.

The Xena data is not integer counts because they [UCSC Xena] increment (+1) the raw HTSeq counts from Genomic Data Commons (GDC), and then log [base 2] transform these.

It is perfectly fine to revert these back to their original form, and then round to 0 decimal places.


ADD COMMENTlink written 7 months ago by Kevin Blighe53k

Yes that was me. Thank you for your time and confirming on the matter.

ADD REPLYlink written 7 months ago by english.server160
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