Question: FireBrowse TCGA data files
0
gravatar for immunogirl2
3 months ago by
immunogirl220
immunogirl220 wrote:

Which FireBrowse file type (TCGA RNAseq data) is suitable to be used with DESeq2. When I use 'RSEM_genes' (unnormalized) file I get 'not all values integer' msg.please see the image

rna-seq R • 178 views
ADD COMMENTlink modified 3 months ago by Shalu Jhanwar470 • written 3 months ago by immunogirl220
1
gravatar for Shalu Jhanwar
3 months ago by
Shalu Jhanwar470
Switzerland
Shalu Jhanwar470 wrote:

It should be Illuminahiseq_rnaseqv2-RSEM_genes_normalized. Have a look at here for details of FireBrowse.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Shalu Jhanwar470
1

Please don't use URL redirectors in answers since they may not be stable. If they become stale then this answer becomes invalid.

ADD REPLYlink written 3 months ago by genomax91k

Totally agree, so I change it to the actual link. Thanks for the reminder.

ADD REPLYlink written 3 months ago by Shalu Jhanwar470

You can use the hyperlink icon in edit window to associate the URL with a word (or a set of words) after highlighting them. Like this.

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax91k

Yeah, that's true, I edited it in the post :)

ADD REPLYlink written 3 months ago by Shalu Jhanwar470

Thank you. One additional Q, do i need to use Tximport with that file or can use this file directly in DESeqdatasetfrommatrix?

ADD REPLYlink written 3 months ago by immunogirl220
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