Question

FireBrowse TCGA data files

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4.4 years ago

immunogirl2 ▴ 20

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 • 1.5k views

ADD COMMENT • link updated 4.4 years ago by Shalu Jhanwar ▴ 540 • written 4.4 years ago by immunogirl2 ▴ 20

score 1 · Answer 1 · 2020-07-22

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4.4 years ago

Shalu Jhanwar ▴ 540

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

ADD COMMENT • link 4.4 years ago by Shalu Jhanwar ▴ 540

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

ADD REPLY • link 4.4 years ago by GenoMax 147k

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

ADD REPLY • link 4.4 years ago by Shalu Jhanwar ▴ 540

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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.

ADD REPLY • link 4.4 years ago by GenoMax 147k

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

ADD REPLY • link 4.4 years ago by Shalu Jhanwar ▴ 540

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

ADD REPLY • link 4.4 years ago by immunogirl2 ▴ 20