Question: How to turn a FPKM table in a matrix that can be analyzed in R?
0
gravatar for JimiOli
9 weeks ago by
JimiOli0
JimiOli0 wrote:

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!

matrix rna-seq deseq fpkm R • 145 views
ADD COMMENTlink modified 8 weeks ago by Carlo Yague2.9k • written 9 weeks ago by JimiOli0

Maybe you can start with this http://www.bioconductor.org/help/workflows/rnaseqGene/#starting-from-count-matrices :)

ADD REPLYlink written 8 weeks ago by Lila M 230

The manuals of edgeR and DESeq2 discuss how to import RNA-seq data for usage by the tool.

ADD REPLYlink written 8 weeks ago by WouterDeCoster17k
2
gravatar for Carlo Yague
8 weeks ago by
Carlo Yague2.9k
Belgium
Carlo Yague2.9k wrote:

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.

ADD COMMENTlink written 8 weeks ago by Carlo Yague2.9k
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