Question: Real-valued HTseq count to DESeq2
0
gravatar for english.server
17 months ago by
Germany
english.server210 wrote:

HI!

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

https://support.bioconductor.org/p/105964/

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 biostars.org real values as count estimates. I am not sure whether it is possible to round data available at

https://xenabrowser.net/datapages/?dataset=TCGA-UCS%2FXena_Matrices%2FTCGA-UCS.htseq_counts.tsv&host=https%3A%2F%2Fgdc.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

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 • 617 views
ADD COMMENTlink modified 17 months ago by Kevin Blighe67k • written 17 months ago by english.server210
2
gravatar for Kevin Blighe
17 months ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k 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.

Kevin

ADD COMMENTlink written 17 months ago by Kevin Blighe67k
1

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

ADD REPLYlink written 17 months ago by english.server210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1903 users visited in the last hour