Question

minfi - error when reading idat files

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stewart999 ▴ 10

@stewart999-11769

Last seen 3.1 years ago

United Kingdom

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 • 4.8k views

ADD COMMENT • link updated 2.3 years ago by Sajad Wani • 0 • written 7.5 years ago by stewart999 ▴ 10

score 1 · Answer 1 · 2017-07-05

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Kasper Daniel Hansen ★ 6.5k

@kasper-daniel-hansen-2979

Last seen 18 months ago

United States

This looks good to me. You don't get an error with force=TRUE. What you're seeing is that you have two sets of IDAT files scanned with different scan settings (specifically with different DMAP files). We see this a lot with the EPIC array. It is unfortunate that Illumina has released some many DMAP files and so many different annotation versions for this array, but that's how it is. Best, Kasper On Wed, Jul 5, 2017 at 11:32 AM, stewart999 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User stewart999 <https: support.bioconductor.org="" u="" 11769=""/> wrote Question: > minfi - error when reading idat files > <https: support.bioconductor.org="" p="" 97773=""/>: > > 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 > > > > ------------------------------ > > Post tags: minfi, methylation > > You may reply via email or visit minfi - error when reading idat files >

ADD COMMENT • link 7.5 years ago Kasper Daniel Hansen ★ 6.5k

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So, Wondering, what is the conclusion, is it ok to use force=TRUE, in the above-mentioned case?

ADD REPLY • link 2.3 years ago thind.amarinde • 0

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I am too struggling with this. is it ok to use force=TRUE?

ADD REPLY • link 2.3 years ago Sajad Wani • 0

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I would expect the discussion above to be pretty clear: There are different types of IDAT files around for the EPIC array because Illumina released a couple of different DMAP files (used to scan the microarrays) and these DMAP files produces IDAT files with almost the same - but not exactly the same - number of probes. Note that the IDAT files themselves don't contain a clear ID for what array type they are, so in minfi we make an educated guess based on the number of probes.

In case you read a set of IDAT files where some of the files have different number of probes, the default behavior is for minfi to throw an error. You can override the error by setting force=TRUE which will create an R object containing all the probes which are present on all of the arrays (which is usually the smaller set). This argument is partly needed because (as I say above) the array type is not encoded in the IDAT file so we are doing some degree of educated guess work. Also, force=TRUE overrides some checks and I think it is possible to merge a 27k array with an EPIC array which would probably NOT be what you would ever want to do.

Does this answer the questions?

ADD REPLY • link 2.3 years ago Kasper Daniel Hansen ★ 6.5k

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Thanks for response. it was helpful

ADD REPLY • link 2.3 years ago Sajad Wani • 0