Hi,
your CDF is most likely corrupt. You didn't tell us what
cdf <- AffymetrixCdfFile$byChipType("HTHGU133A_Hs_ENTREZG");
print(cdf);
outputs, and also not how you obtained that CDF. However, it looks
like (it originates from) a custom CDF by the BrainArray project
[http://brainarray.mbni.med.umich.edu/]. Some of their releases have
invalid CDF headers, cf. thread '[customcdf] ENTREZG, AUGUSTUST for
pig species is updated' on May 8, 2012 [http://goo.gl/Xg1pp]. Also,
if you've used one of their invalid versions, you should have gotten
an error message when you tried to convert it to a binary CDF.
I've checked, the v1.16.0 release of HTHGU133A_Hs_ENTREZG.cdf *is
valid* - try that instead.
Hope this helps
Henrik
On Thu, Oct 18, 2012 at 6:45 AM, MarcinS <siat...@gmail.com> wrote:
> Dear aroma.affymetrix users,
>
> I am using fit function for RmaPlm object and I am getting this error:
>
> Error in .subset2(groups, 1) : subscript out of bounds
>
> cdf file was obtained from brainarray website, version 16
>
> here is the code:
>
>>library(aroma.affymetrix)
>>verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>>hthgu133aCdf <- AffymetrixCdfFile$byChipType("HTHGU133A_Hs_ENTREZG")
>>hthgu133aBatch<-AffymetrixCelSet$byName("ConnectivityMap",
>> cdf=hthgu133aCdf)
>
>>hthgu133aBatch
>
> AffymetrixCelSet:
>
> Name: ConnectivityMap
>
> Tags:
>
> Path: rawData/ConnectivityMap/HTHGU133A_Hs_ENTREZG
>
> Platform: Affymetrix
>
> Chip type: HTHGU133A_Hs_ENTREZG
>
> Number of arrays: 6026
>
> Names: 5500024017802120306174.A01, 5500024017802120306174.A02,
> 5500024017802120306174.A03, ..., 5500024053146032309538.H12 [6026]
>
> Time period: [not reported if more than 500 arrays]
>
> Total file size: 31816.39MB
>
> RAM: 5.11MB
>
>>bc.hthgu133a<-RmaBackgroundCorrection(hthgu133aBatch)
>>hthgu133aBC<-process(bc.hthgu133a, verbose=verbose)
>>qn.hthgu133a<-QuantileNormalization(hthgu133aBC, typesToUpdate="pm")
>>hthgu133aN<-process(qn.hthgu133a, verbose=verbose)
>
>>hthgu133aN
>
> AffymetrixCelSet:
>
> Name: ConnectivityMap
>
> Tags: RBC,QN
>
> Path: probeData/ConnectivityMap,RBC,QN/HTHGU133A_Hs_ENTREZG
>
> Platform: Affymetrix
>
> Chip type: HTHGU133A_Hs_ENTREZG
>
> Number of arrays: 6026
>
> Names: 5500024017802120306174.A01, 5500024017802120306174.A02,
> 5500024017802120306174.A03, ..., 5500024053146032309538.H12 [6026]
>
> Time period: [not reported if more than 500 arrays]
>
> Total file size: 31816.39MB
>
> RAM: 5.11MB
>
>>hthgu133aNPlm<-RmaPlm(hthgu133aN)
>>hthgu133aNPlmFit<-fit(hthgu133aNPlm, verbose=verbose)
> [...]
>
> 20121018 15:26:57| Chunk #1 of 1...done
>
> 20121018 15:26:57| lapplyInChunks()...done
>
> 20121018 15:26:57| Reading cell indices from CDF file...done
>
> used (Mb) gc trigger (Mb) max used (Mb)
>
> Ncells 5894795 314.9 9040660 482.9 9040660 482.9
>
> Vcells 6325253 48.3 10339736 78.9 9309810 71.1
>
> 20121018 15:26:58| readUnits.AffymetrixCdfFile(): Updating cache
>
> 20121018 15:26:59| Reading CDF cell indices...done
>
> 20121018 15:26:59| Extracting first CDF group for each unit...
>
> Error in .subset2(groups, 1) : subscript out of bounds
>
> 20121018 15:26:59| Extracting first CDF group for each unit...done
>
> 20121018 15:26:59| Chunk #1 of 1...done
>
> 20121018 15:26:59| lapplyInChunks()...done
>
> 20121018 15:26:59| Identifying CDF units...done
>
> 20121018 15:26:59| Identifying non-fitted units in chip-effect file...done
>
> 20121018 15:26:59| Identifying non-estimated units...done
>
> 20121018 15:26:59|Fitting model of class RmaPlm...done
>
>
> and then it stops.
>
> here is sessionInfo():
>
> R version 2.15.1 (2012-06-22)
>
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
>
> locale:
>
> [1] pl_PL.UTF-8/pl_PL.UTF-8/pl_PL.UTF-8/C/pl_PL.UTF-8/pl_PL.UTF-8
>
>
> attached base packages:
>
> [1] stats graphics grDevices utils datasets methods base
>
>
> other attached packages:
>
> [1] aroma.affymetrix_2.6.0 affxparser_1.30.0 aroma.apd_0.2.3
> R.huge_0.4.1 aroma.light_1.28.0 aroma.core_2.6.0
> matrixStats_0.5.3 R.rsp_0.8.2
>
> [9] R.cache_0.6.3 R.devices_2.1.1 R.filesets_1.1.5
> digest_0.5.2 R.utils_1.16.2 R.oo_1.9.9
> R.methodsS3_1.4.2
>
>
> loaded via a namespace (and not attached):
>
> [1] tools_2.15.1
>
>
>
> Thank you for help
> Marcin Siatkowski
>
>
>
>
>
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
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