Question: error using EPIC early access version arrays with minfi
0
gravatar for mcastrod
3.0 years ago by
mcastrod0
mcastrod0 wrote:

Dear all,

We are having some problems with the analysis of some EPIC methylation arrays (early access version) with minfi package. These arrays contains less cpgs than the current arrays so the annotation files are different.

When we tried to load the arrays with read.metharray function we get the error:

RGChannelSet (storageMode: lockedEnvironment)
assayData: 1032279 features, 1 samples
  element names: Green, Red
An object of class 'AnnotatedDataFrame': none
Annotation
  array: Unknown
  annotation: XX

We tried to create a new annotation object with the illumina bpm file and modify the read.metharray function but we obtained several incompatibility errors with the new annotation. Anyone knows how to create and attach the annotation required by minfi functions or how to deal with this kind of epic arrays?

Thank you very much.

 

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by mcastrod0
Answer: error using EPIC early access version arrays with minfi
0
gravatar for Kasper Daniel Hansen
3.0 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
Similar stuff has been reported and has usually been solved by rescanning the arrays using updated scanner files from Illumina. If you can, I would like to see an example array (both Red and Green channels, so 2 IDAT files) Best, Kasper On Thu, Jun 16, 2016 at 1:56 PM, mcastrod [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User mcastrod <https: support.bioconductor.org="" u="" 10187=""/> wrote Question: > error using EPIC early access version arrays with minfi > <https: support.bioconductor.org="" p="" 83932=""/>: > > Dear all, > > We are having some problems with the analysis of some EPIC methylation > arrays (early access version) with minfi package. These arrays contains > less cpgs than the current arrays so the annotation files are different. > > When we tried to load the arrays with read.metharray function we get the > error: > > RGChannelSet (storageMode: lockedEnvironment) > assayData: 1032279 features, 1 samples > element names: Green, Red > An object of class 'AnnotatedDataFrame': none > Annotation > array: Unknown > annotation: XX > > We tried to create a new annotation object with the illumina bpm file and > modify the read.metharray function but we obtained several incompatibility > errors with the new annotation. Anyone knows how to create and attach the > annotation required by minfi functions or how to deal with this kind of > epic arrays? > > Thank you very much. > > > > ------------------------------ > > Post tags: epic, minfi, read.metharray, software error > > You may reply via email or visit error using EPIC early access version arrays with minfi >
ADD COMMENTlink written 3.0 years ago by Kasper Daniel Hansen6.4k
Answer: error using EPIC early access version arrays with minfi
0
gravatar for mcastrod
3.0 years ago by
mcastrod0
mcastrod0 wrote:

Thank you Kasper,

We will try to rescan the arrays as you said. We will also send you today an idat file example.

Best,

Manuel

 

ADD COMMENTlink written 3.0 years ago by mcastrod0
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