Question

[read.metharray] Trying to parse different IDAT files, of different size and type.

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researcher • 0

@researcher-20723

Last seen 21 months ago

United States

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 • 1.3k views

ADD COMMENT • link updated 4.8 years ago by Gordon Smyth 50k • written 4.8 years ago by researcher • 0

score 0 · Answer 1 · 2019-06-19

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Gordon Smyth 50k

@gordon-smyth

Last seen 1 hour ago

WEHI, Melbourne, Australia

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 COMMENT • link 4.8 years ago Gordon Smyth 50k

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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 REPLY • link 4.8 years ago Kasper Daniel Hansen ★ 6.5k