Entering edit mode
Hi
I am reading 1000 EPIC samples using minfi's read.metharray.exp() function as follows:
RGset <- read.metharray.exp(base=NULL, targets=targets, verbose=TRUE, extended=TRUE)
The error I receive at the end of this process is:
... [read.metharray] Creating data matrices ... Error in read.metharray(files, extended = extended, verbose = verbose, : [read.metharray] Trying to parse IDAT files with different array size but seemingly all of the same type. You can force this by 'force=TRUE', see the man page ?read.metharray
If I use the force=TRUE flag it reads the idats OK. I was wondering why I am receiving this error and if it may indicate that there are problems with the raw data
I have used the readIDAT function to determine the number of probes in my idats and they are within the permissible range: 320 idats have 1051815 probes and 1680 idats have 1051943 probes
Thanks
-Stewart