Question: Rna Raw Count Data Normalization
0
gravatar for jack
5.6 years ago by
jack450
jack450 wrote:

Hi,

I have raw count data of RNA seq. I want to normalize it . which normalization methods do you recommend and which R packages I can use ?

ADD COMMENTlink modified 5.6 years ago by Devon Ryan90k • written 5.6 years ago by jack450
3
gravatar for Devon Ryan
5.6 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

DESeq2, edgeR and limma (with voom()) are the common choices. They all have default normalization methods that you might as well stick with unless you know enough to judge how well they're working (which, if you're asking this question, is presumably not the case). I personally prefer DESeq2, but some designs are more easily accomplished with limma.

ADD COMMENTlink written 5.6 years ago by Devon Ryan90k

used DESeq2, and I want to do log transformation. I've got this error. what should I do? rld <- rlogTransformation(my_rawcount, blind=TRUE)

the error is : Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘sizeFactors’ for signature ‘"matrix"’

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by jack450
3

You're giving a matrix to a function that expects a DESeqDataSet object. Try creating the appropriate object first, likely with the DESeqDataSetFromMatrix() function.

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by Devon Ryan90k
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