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


ADD COMMENTlink modified 4 months ago • written 23 months ago by Kevin Blighe65k
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