Question: [read.metharray] Trying to parse different IDAT files, of different size and type.
0
3 months ago by
researcher0 wrote:

Hi All, I am trying to analyze methylation data from 3 different runs (a mix of 450K and 2 different versions of EPIC array) together. Even after using "force=TRUE" with read.metharray.exp() but getting the following error:

Error in read.metharray(basenames = files, extended = extended, verbose = verbose,  :
[read.metharray] Trying to parse different IDAT files, of different size and type.
Execution halted


Any help or clue will be highly appreciated. Thanks in advance.

limma minfi • 90 views
modified 3 months ago by Gordon Smyth38k • written 3 months ago by researcher0
Answer: [read.metharray] Trying to parse different IDAT files, of different size and ty
0
3 months ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

I'm not the minfi author, but the error message seems self-explanatory to me. You can't read a mix of three different types of arrays using one read command. All the arrays need to be of the same type, even if some variation in the number of probes is allowed.

If these are indeed the same arrays, but just with slightly different number of beads, then it should work. If not, then it shouldn't (Ie you cannot read in 450k and EPIC together). It is hard to know which case it is. If you want more help, you should make (some of) the idat files available on dropbox so I can take a look.

Best, Kasper