Question: Differential Expression Gene analysis using normalized data
0
gravatar for oghzzang
16 months ago by
oghzzang40
oghzzang40 wrote:

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?

rna-seq • 528 views
ADD COMMENTlink modified 16 months ago by noorpratap.singh270 • written 16 months ago by oghzzang40
0
gravatar for noorpratap.singh
16 months ago by
India
noorpratap.singh270 wrote:

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

ADD COMMENTlink written 16 months ago by noorpratap.singh270

Thanks a lot Singh.

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

ADD REPLYlink modified 16 months ago • written 16 months ago by oghzzang40
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