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Question: minfi - error when reading idat files
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gravatar for stewart999
4 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

 

ADD COMMENTlink modified 4 months ago by Kasper Daniel Hansen6.3k • written 4 months ago by stewart99910
0
gravatar for Kasper Daniel Hansen
4 months ago by
United States
Kasper Daniel Hansen6.3k wrote:
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 COMMENTlink written 4 months ago by Kasper Daniel Hansen6.3k
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