Question: Error when reading in idat files using methylumi package
0
gravatar for amjass
9 months ago by
amjass20
amjass20 wrote:

Hi all,

I was wondering if anybody has used the methylumi package and has read in idat files using the methylumIDAT function.

I have tried to read in idat files by pointing R to the the folder containing idat files, and also have a metadata csv files in this folder. My code is as follows:

dir<-"temp methylation/"
pd<-read.csv("temp methylation/meta.csv")

library(methylumi)

methy<-methylumIDAT(barcodes = pd$barcodes, pdat = pd, 
             idatPath = dir, oob = TRUE)

After running the code above i get the following error message:

0 HumanMethylation27 samples found 30 HumanMethylation450 samples found number of rows of result is not a multiple of vector length (arg 1)Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent

The dim of pd are: dim(pd) = 30 13

and as you can see, 30 methylation450 samples are successfully found. I am unsure as to why I am getting this error message and any help would be much appreciated! I am happy to provide additional information if required!!

Thanks!

ADD COMMENTlink modified 9 months ago • written 9 months ago by amjass20
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