RNA sequencing analysis

Question

[bioinformatics]

Hi,

I'm trying to perform RNA sequencing analysis using data download from NCBI: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE184199

I'm following this workflow: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934518/

These are the commands I've done so far:

FileURL <- paste(           "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE184199",
            "format=file",
            "file=GSE184199_ALL_exp_FPKM.txt.gz",
            sep="&")
          download.file(FileURL, "GSE184199_ALL_exp_FPKM.txt.gz")

However, when I try to run the next command line I get an error message:

GenewiseCounts <- read.delim("GSE184199_ALL_exp_FPKM.txt.gz", row.names="EntrezGeneID")
Error in data[[rowvar]] : 
  attempt to select less than one element in get1index

Does anyone know how I might correct this?

Thanks!

Answer 1

[swbarnes2]

Your tutorial does not say to use FPKM. EdgeR takes raw counts, not FPKM. Even if you could get it to work...don't.

If you must use this data, you can't use this tutorial. You need to look up a limma or limma-zoom tutorial.

[bioinformatics]

Ok thanks for your advise. I will try to follow a limma-zoom tutorial.

[ATpoint]

Don't use voom on fpkm, this has been asked many times before: https://support.bioconductor.org/p/56275/#56299