Question: How to turn a FPKM table in a matrix that can be analyzed in R?
0
gravatar for JimiOli
9 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 • 395 views
ADD COMMENTlink modified 9 months ago by Carlo Yague3.5k • written 9 months ago by JimiOli0

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

ADD REPLYlink written 9 months ago by Lila M 370

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

ADD REPLYlink written 9 months ago by WouterDeCoster24k
2
gravatar for Carlo Yague
9 months ago by
Carlo Yague3.5k
Belgium
Carlo Yague3.5k 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 9 months ago by Carlo Yague3.5k
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