Question: FuntooNorm on 450K and Epic data combined RGSet
0
gravatar for poojitha.stemcell
2.2 years ago by
poojitha.stemcell0 wrote:

I am trying to perform funtooNorm on a RGSet object, that has samples run on 450K and EPIC arrays. I combined the two objects using combineArrays function in minfi. I am able to perform funtooNorm on 450K data object separately, but not on EPIC data or combined data object. I get the following error message.

mySampleSet <- fromRGChannelSet(RGSet_combined)
Error in minfi::getRed(myRGChannelSet)[controlTable$Address, ] : 
  subscript out of bounds

I am using R 3.4 and all my packages are updated. I have checked the "cell_type" field in pheno data. Could anyone help me resolve this issue?

Regards,

Poojitha

ADD COMMENTlink modified 18 months ago by simon_10120 • written 2.2 years ago by poojitha.stemcell0

I've encountered the same error, any idea how to solve this?

ADD REPLYlink written 18 months ago by simon_10120
Answer: FuntooNorm on 450K and Epic data combined RGSet
0
gravatar for Kasper Daniel Hansen
2.2 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
The authors of funtooNorm should modify their code to work with subsetted objects. This is something we now fully support in minfi and they can look in minfi to see examples of how to write it. One advantage of working with subsetted objects is to allow things like this. Best, Kasper On Tue, Jun 20, 2017 at 8:06 AM, poojitha.stemcell [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User poojitha.stemcell <https: support.bioconductor.org="" u="" 11859=""/> wrote Question: > FuntooNorm on 450K and Epic data combined RGSet > <https: support.bioconductor.org="" p="" 97229=""/>: > > I am trying to perform funtooNorm on a RGSet object, that has samples run > on 450K and EPIC arrays. I combined the two objects using combineArrays > function in minfi. I am able to perform funtooNorm on 450K data object > separately, but not on EPIC data or combined data object. I get the > following error message. > > mySampleSet <- fromRGChannelSet(RGSet_combined) > Error in minfi::getRed(myRGChannelSet)[controlTable$Address, ] : > subscript out of bounds > > I am using R 3.4 and all my packages are updated. I have checked the > "cell_type" field in pheno data. Could anyone help me resolve this issue? > > Regards, > > Poojitha > > ------------------------------ > > Post tags: funtooNorm, minfi, illuminahumanmethylationepicanno.ilmn10b.hg19 > > > You may reply via email or visit FuntooNorm on 450K and Epic data combined RGSet >
ADD COMMENTlink written 2.2 years ago by Kasper Daniel Hansen6.4k

I've encountered the same error, any idea how to solve this?

ADD REPLYlink written 18 months ago by simon_10120
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