Question: [read.metharray] Trying to parse different IDAT files, of different size and type.
0
gravatar for researcher
3 months ago by
researcher0
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.
Calls: read.metharray.exp -> read.metharray
Execution halted

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

limma minfi • 90 views
ADD COMMENTlink 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
gravatar for Gordon Smyth
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.

ADD COMMENTlink written 3 months ago by Gordon Smyth38k

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

ADD REPLYlink written 3 months ago by Kasper Daniel Hansen6.4k
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