Question: why are RNA-seq fkpm of TCGA PAN-cancer normal and primary tumor are the same
1
gravatar for zany1983
6 weeks ago by
zany198310
zany198310 wrote:

I was going to compare gene expression in primary tumor and normal control.

So I downloaded PAN cancer data from xena.USCS.edu (https://tcga.xenahubs.net/download/TCGA.PANCAN.sampleMap/PANCAN_clinicalMatrix for clinical matrix and
https://toil.xenahubs.net/download/tcga_RSEM_gene_fpkm for gene expression TOIL Gene RSEM fpkm dataset.

Then I selected patient that have matched normal and primary tumor sample types, and I found that for each gene, fpm from normal and primary tumor are JUST THE SAME!

I wonder what's wrong with this.

Is there anybody helping me? Thanks in advance!

rna-seq fkpm tcga • 152 views
ADD COMMENTlink modified 6 weeks ago by Chris Miller18k • written 6 weeks ago by zany198310
2
gravatar for Chris Miller
6 weeks ago by
Chris Miller18k
Washington University in St. Louis, MO
Chris Miller18k wrote:

In almost all cases cases, each TCGA patient only had tumor RNAseq done. (see previous discussions). Are you sure that there was actually normal RNAseq available, or have you pulled down the same file twice through different linkages?

ADD COMMENTlink written 6 weeks ago by Chris Miller18k

Yes, I noticed much more number of tumor than control, with many of patient having only tumor data. However, I have filtered the data from above mentioned link to make sure that each patient have both normal and primary tumor sample IDs.

I'm sure that I downloaded the intact file (https://toil.xenahubs.net/download/tcga_RSEM_gene_fpkm )only once

I'm wondering if any other person also encountered this problem? Or, should I check other portals?

ADD REPLYlink written 6 weeks ago by zany198310
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