Question: Differential Expression Gene analysis using normalized data
0
gravatar for oghzzang
12 months ago by
oghzzang30
oghzzang30 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 • 423 views
ADD COMMENTlink modified 12 months ago by noorpratap.singh240 • written 12 months ago by oghzzang30
0
gravatar for noorpratap.singh
12 months ago by
India
noorpratap.singh240 wrote:

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

ADD COMMENTlink written 12 months ago by noorpratap.singh240

Thanks a lot Singh.

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

ADD REPLYlink modified 12 months ago • written 12 months ago by oghzzang30
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