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?
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oghzzang •
I can't help with analysing normalised data but you could use TCGABiolinks for downloading raw count data from TCGA.
Thanks a lot Singh.
My data is driven patients. (no TCGA data.) And there is only rsem quartile normalized data.
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Hello Oghzzang,
Did you figure out how to get DEGs using rsem normalized data? I am currently having the same issue.
Thank you
This bioconductor post may help.