Question: minfi - error when reading idat files
0
24 months ago by
stewart99910
stewart99910 wrote:

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

minfi methylation • 581 views
modified 24 months ago by Kasper Daniel Hansen6.4k • written 24 months ago by stewart99910
0
24 months ago by
United States
Kasper Daniel Hansen6.4k wrote: