Data object format for deseq2
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@timivanov92-14799
Last seen 2.7 years ago

Hey, can anyone help me? 

I'm very new to R and i'm trying to perform differential expression analysis on files, obtained from RSEM.

So i have 8 files (4 experiment and 4 control). These files each has "expected_counts" columns (which is not an integer, btw, is it ok?)

And i'm having a bad time adjusting my data to right format for deseq2 package. 

Can i mb see an actual format for input data, so i would create such a file by python script? 

deseq2 R RSEM • 635 views
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@mikelove
Last seen 2 days ago
United States

Take a look at the following section of the RNA-seq workflow for beginner's to R:

http://www.bioconductor.org/help/workflows/rnaseqGene/#deseq2-import-functions

You can import from these various formats. If you have RSEM output files, you can use tximport() followed by DESeqDataSetFromTximport.

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