Differential Expression Gene analysis using normalized data

Question

[oghzzang]

Hello.

I'm working on RNA expression data from TCGA's pipeline. we have 'rsem_isoforms_normalized.txt', 'rsem_gene_normalized.txt'.

I know DESeq and EdgeR are used to DEG analysis. But I don't have raw count data.

what can I do for DEG analysis using rsem normalized data?

[Ety]

Hello Oghzzang,

Did you figure out how to get DEGs using rsem normalized data? I am currently having the same issue.

Thank you

[Friederike]

This bioconductor post may help.

Answer 1

[noorpratap.singh]

I can't help with analysing normalised data but you could use TCGABiolinks for downloading raw count data from TCGA.

[oghzzang]

Thanks a lot Singh.

My data is driven patients. (no TCGA data.) And there is only rsem quartile normalized data.