Question: Minfi error when using force=TRUE in read.metharray
0
gravatar for jbar3141
16 months ago by
jbar31410
jbar31410 wrote:

Hi, I am trying to read some EPIC arrary data using:

targets <- read.metharray.sheet(data_dir)
RGset <- read.metharray.exp(targets = targets, verbose = TRUE, force=TRUE)

and I get the following error

[read.metharray] Instantiating final object ...

Error in `sampleNames<-`(`*tmp*`, value = c("1600101", "1600111", "1600115",  :

  number of new names (1051943) should equal number of rows in AnnotatedDataFrame (1051539)

Calls: read.metharray.exp ... featureNames<- -> featureNames<- -> sampleNames<- -> sampleNames<-

Execution halted

I used the force=TRUE option because I was getting the same error as described hereĀ minfi - error when reading idat files.

Thanks in advance.

minfi methylation epic • 299 views
ADD COMMENTlink written 16 months ago by jbar31410

Please include the output of sessionInfo() otherwise we don't know what version of R or minfi you are using. Please also read http://www.bioconductor.org/help/support/posting-guide/ for advice on creating a question that will be easier for people to help you answer.

ADD REPLYlink modified 16 months ago • written 16 months ago by Peter Hickey460

I believe this is cross-posted from https://github.com/hansenlab/minfi/issues/173. Based on the sessionInfo() you posted there, you are using an old version of minfi. As recommended in http://www.bioconductor.org/help/support/posting-guide/, please try updating to the latest version (see http://www.bioconductor.org/install/).

ADD REPLYlink modified 16 months ago • written 16 months ago by Peter Hickey460

Yes my mistake, new version works fine. Many thanks.

ADD REPLYlink written 16 months ago by jbar31410
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