Error when trying to read in idat files in methylumi
0
0
Entering edit mode
A ▴ 40
@a-14337
Last seen 10 months ago
United Kingdom

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!

methylumi 450k methylation methylome • 850 views
ADD COMMENT

Login before adding your answer.

Traffic: 598 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6