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Help locating TCGA data from cbioportal

Hi,

I am a newbie, I want to locate the following files:

  • data_RNA_Seq_v2_expression_median.txt
  • data_linear_CNA.txt

From what I read from other threads/google search, these data are supposed to come from cbioportal? But I can't seem to locate these files in the cbioportal website!

Any help is appreciated :)

Thanks!

cancer tcga rna cbioportal cna
• 2,436 views • link
written by ConvolutedGenome • ConvolutedGenome

Thanks,

What do you mean by selecting 'RNAseq'? there is no such selection

My cancer of interest is melanoma, the only download button that I can locate is the one circled here (is this it?)

melanoma TCGA firehose legacy from cbioportal

Thank you

• 0 views • link
written by ConvolutedGenome • ConvolutedGenome

Thank you,

I have downloaded all data from Skin Cutaneous Melanoma (TCGA, Firehose Legacy)

I was able to locate "data_linear_cna.txt" (highlighted below), but "data_RNA_Seq_v2_expression_median.txt" is missing

I am almost sure that "data_RNA_Seq_v2_expression_median.txt" is renamed to "data_mrna_seq_v2_rsem.txt"

idk why they do this

enter image description here

• 0 views • link
written by ConvolutedGenome • ConvolutedGenome

These are old version of the TCGA data. There are better ones from the most recent TCGA PanCan analysis, unless you have a particular reason to stick to this version.

• 0 views • link
written by Zhenyu Zhang Zhenyu Zhang

I want those exact files, because I want to replicate the method of a paper

Now this paper only supply the file name without telling me where to find it, so I've been looking for those exact files everywhere on the internet

• 0 views • link
written by ConvolutedGenome • ConvolutedGenome

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