Is it possible that someone can share all the TCGA cancer data in Excel?

Question

[sxs870917]

Is it possible that someone can share all the TCGA cancer data in Excel?

Many thanks.

[Pierre Lindenbaum]

[lieven.sterck]

wild guess? : no

correct answer:: you simply should not! ;)

[ATpoint]

Please be more specific. What do you need? Raw data or analyzed files and what type of data? Expression profiles, methylation etc? Did you search the TCGA data portal already? How To Ask Good Questions On Technical And Scientific Forums

[sxs870917]

I just need expression data of each cancer types separately.

[WouterDeCoster]

Then you should have written that, we cannot read your mind :)

[Kevin Blighe]

For 'ready made' TCGA data, take a look at:

• UCSC Xena
• MSKCC cBioPortal
• Broad Institute's FireBrowse

These comprise re-processed data, so, you are limited to using data produced by methods chosen by these third parties. For most general usage, this data is fine.

Answer 1

[GenoMax]

LinkedOmics is another portal for processed TCGA data.

[sxs870917]

Thanks! ~~~~~ Absolutely solve my problem!

[WouterDeCoster]

I have moved the comment of @Genomax to an answer so you can mark is as accepted as it solved your question.

[sxs870917]

Take one column name, for example, TCGA.OR.A5J1.

How do I know which one is control and which one is cancer?

[Kevin Blighe]

You cannot distinguish tumour from normal from just the short TCGA barcode, i.e., TCGA.OR.A5J1. You need the full barcode. Take a look: A: Meaning letters in TCGA sample barcode field

[sxs870917]

Oh, god. It means I still can analyze it.

I don't know what happens to RTCGA, some cancer types just cannot be downloaded.

[Kevin Blighe]

What do you mean?

You have a linked thread relating to RTCGA: Do some cancer type data in RTCGA cannot be downloaded?