Help locating TCGA data from cbioportal

Question

[ConvolutedGenome]

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!

[GenoMax]

You will need to find the cancer type you want to work with. Select RNAseq data type and then there are download icons that you will find on the page that should allow you to get the data. Here is an example page: https://www.cbioportal.org/study/summary?id=luad_tcga_pub

[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?)

Thank you

[GenoMax]

There is RNAseq data with skin cutaneous melanoma: https://www.cbioportal.org/study/summary?id=skcm_tcga_pan_can_atlas_2018

If you search for melanoma there are multiple types : https://www.cbioportal.org/datasets

[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

[Zhenyu Zhang]

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.

[ConvolutedGenome]

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