Question: Differential Expression Gene analysis using normalized data
0
gravatar for oghzzang
2.6 years 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 • 841 views
ADD COMMENTlink modified 2.6 years ago by noorpratap.singh300 • written 2.6 years ago by oghzzang40
0
gravatar for noorpratap.singh
2.6 years ago by
University of Maryland
noorpratap.singh300 wrote:

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

ADD COMMENTlink written 2.6 years ago by noorpratap.singh300

Thanks a lot Singh.

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

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by oghzzang40
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