Question: How to turn a FPKM table in a matrix that can be analyzed in R?
0
gravatar for JimiOli
18 months 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 • 949 views
ADD COMMENTlink modified 18 months ago by Carlo Yague4.2k • written 18 months ago by JimiOli0

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

ADD REPLYlink written 18 months ago by Lila M 390

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

ADD REPLYlink written 18 months ago by WouterDeCoster32k
2
gravatar for Carlo Yague
18 months ago by
Carlo Yague4.2k
Belgium
Carlo Yague4.2k 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 18 months ago by Carlo Yague4.2k
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