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FireBrowse TCGA data files

Which FireBrowse file type (TCGA RNAseq data) is suitable to be used with DESeq2. When I use 'RSEM_genes' (unnormalized) file I get 'not all values integer' msg.please see the image

r rna-seq
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updated by Shalu Jhanwar Shalu Jhanwar • written by immunogirl2 • immunogirl2

1 answer

It should be Illuminahiseq_rnaseqv2-RSEM_genes_normalized. Have a look at here for details of FireBrowse.

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written by Shalu Jhanwar Shalu Jhanwar

Please don't use URL redirectors in answers since they may not be stable. If they become stale then this answer becomes invalid.

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written by GenoMax GenoMax

Totally agree, so I change it to the actual link. Thanks for the reminder.

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written by Shalu Jhanwar Shalu Jhanwar

You can use the hyperlink icon in edit window to associate the URL with a word (or a set of words) after highlighting them. Like this.

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written by GenoMax GenoMax

Yeah, that's true, I edited it in the post :)

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written by Shalu Jhanwar Shalu Jhanwar

Thank you. One additional Q, do i need to use Tximport with that file or can use this file directly in DESeqdatasetfrommatrix?

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written by immunogirl2 • immunogirl2

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