Question: RNA-Seq data from Firebrowse TCGA
0
gravatar for landscape95
23 months ago by
landscape95170
landscape95170 wrote:

Hi, I am building the logistic regression between radiotherapy clinical data (yes/no) and gene expression for the probability of assigning RT to patients from RNA-Seq from Firebrowse TCGA Breast cancer RSEM normalized, but I think it the values of the genes vary a lot (please have a look in the picture). Should I do any normalization to balance between these gene expression? Thanks a lot!

enter image description here

rna-seq • 1.2k views
ADD COMMENTlink modified 23 months ago • written 23 months ago by landscape95170
2
gravatar for Kevin Blighe
23 months ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

I would import these RSEM gene-level [estimated] counts to DESeq2 either manually or via tximport. This is mentioned in the vignette. In DESeq2, I would normalise them with RT in my design formula and then transform these normalised counts to regularised log expression levels with blind = FALSE, i.e., rlog(dds, blind = FALSE).

It is those transformed, normalised expression levels on which I would conduct my downstream regression analysis.

Kevin

ADD COMMENTlink modified 4 months ago • written 23 months ago by Kevin Blighe65k
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: 1252 users visited in the last hour