How to turn a FPKM table in a matrix that can be analyzed in R?
I want to transform my FPKM table (RNA-seq data) into a matrix, so that I can analyze the gene expression data in R, I was wondering which tool to use and how? And how to import this matrix output by DEseq or EdgeR?
Thank you!
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Carlo Yague
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JimiOli •
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JimiOli •
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I was wondering which tool to use and how?
Try the read.table function in R.
And how to import this matrix output by DEseq or EdgeR?
I'm not sure to understand, but if you want to use FPKM data in DEseq or EdgeR, this is a bad idea. Those tools require raw counts as input.
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Maybe you can start with this http://www.bioconductor.org/help/workflows/rnaseqGene/#starting-from-count-matrices :)
The manuals of edgeR and DESeq2 discuss how to import RNA-seq data for usage by the tool.