Question: RNA-Seq data from Firebrowse TCGA
gravatar for landscape95
6 months ago by
landscape95160 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 • 502 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by landscape95160
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe42k
Republic of Ireland
Kevin Blighe42k wrote:

I would import these RSEM gene-level 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 counts with blind=FALSE, i.e., rlog(dds, blind=FALSE).

It is on those transformed, normalsied counts on which I would conduct my regression analysis.


ADD COMMENTlink written 6 months ago by Kevin Blighe42k
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