Trying to do log2 transformation of my rna seq data
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7 months ago
rishav513 • 0

While trying to log transform my RNA seq data, I got this error

> log_counts <- log2(hep + 1)
Error in FUN(left, right) : non-numeric argument to binary operator

Even after removing my first column, I got the same error

> log_counts <- log2(hep[,-1] + 1)
Error in FUN(left, right) : non-numeric argument to binary operator

My "hep" data is as follows:

please see the link below for image of "hep" data

R • 786 views
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Your columns are probably not a numeric datatype. What is class(hep$A1)?

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class(hep$A1)

[1] "character"

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Well, there you go. Try this:

log2_counts <- log2(data.matrix(hep[,-1]))
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you can do it inside deseq2

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7 months ago
Gordon Smyth ★ 3.6k

Log-transforming RNA-seq counts is nonsense and will give poor results in any analysis, as you indeed seem to report for this data on Biconductor:

https://support.bioconductor.org/p/9136077/

Please follow one of our workflows for an appropriate analysis of RNA-seq data.

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