Question: arrayQualityMetrics 3.2.0 in Bioc release 2.7 is broken
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gravatar for Wolfgang Huber
8.7 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
This will manifest itself by seeing the error message Error in aqm.highlight(doc, annotationInfo = annotationInfo) : 'length(annotationInfo$annotation)' must be equal to 'length(series)', the number of objects in the plot. The reason appears to be a misfit between R's SVG-device and the package SVGAnnotation that seems to have entered just a few days before R-2.12.0's release. I am working on a solution and will announce it here. As a workaround until then, please use http://www.bioconductor.org/packages/2.6/bioc/html/arrayQualityMetrics .html (For R-2.12 users: first install the package as usual with "biocLite", then manually download the version above and install it over that.) Sorry for the trouble. Best wishes Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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ADD COMMENTlink modified 8.7 years ago by Mike Walter230 • written 8.7 years ago by Wolfgang Huber13k
Answer: arrayQualityMetrics 3.2.0 in Bioc release 2.7 is broken
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gravatar for Mike Walter
8.7 years ago by
Mike Walter230
Germany
Mike Walter230 wrote:
Dear List, I have a series of golden gate cancer panel SNP data and wanted to use the beadarraySNP package to analyse the data. Unfortunately, I only have the idat files and not the csv files. Thus I tried 'crlmm' package to parse the idats for the red and green channel to create the csv tables. I get some error message which is most likely related to the format of the files. library(ff) library(crlmm) f.GG = list.files() x = crlmm:::readIDATf.GG) Error in matrix(0, nFields, 3) : too many elements specified x = crlmm:::readIdatFiles(path=getwd()) #I know that this is for Infinium data, I tried anyway reading 4075501002_R001_C001 _Grn.idat ? ?? Error in matrix(0, nFields, 3) : too many elements specified Does someone has an idea how to read in the files? Any hint is welcome. Thanks and kind regards, Mike > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] crlmm_1.6.5 oligoClasses_1.10.0 Biobase_2.8.0 [4] ff_2.1-2 bit_1.1-4 loaded via a namespace (and not attached): [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 [4] Biostrings_2.16.9 DBI_0.2-5 ellipse_0.3-5 [7] genefilter_1.30.0 IRanges_1.6.16 mvtnorm_0.9-92 [10] preprocessCore_1.10.0 RSQLite_0.9-2 splines_2.11.1 [13] survival_2.35-8?????? xtable_1.5-6
ADD COMMENTlink written 8.7 years ago by Mike Walter230
Dear Mike, It is my understanding that idats from Illumina's GoldenGate arrays and expression BeadChips are encrypted. The code to read in idat files in crlmm does not deal with encrypted data. To use beadarraySNP, you will need BeadStudio/GenomeStudio output from your experiment (typically one file which contains the intensities and genotype calls from all the samples you are interested in). Best wishes, Matt > Dear List, > > I have a series of golden gate cancer panel SNP data and wanted to use the > beadarraySNP package to analyse the data. Unfortunately, I only have the > idat files and not the csv files. Thus I tried 'crlmm' package to parse > the idats for the red and green channel to create the csv tables. I get > some error message which is most likely related to the format of the > files. > > library(ff) > library(crlmm) > > f.GG = list.files() > > x = crlmm:::readIDATf.GG) > Error in matrix(0, nFields, 3) : too many elements specified > > > x = crlmm:::readIdatFiles(path=getwd()) #I know that this is for Infinium > data, I tried anyway > reading 4075501002_R001_C001 _Grn.idat ? ?? Error in matrix(0, nFields, > 3) : too many elements specified > > Does someone has an idea how to read in the files? Any hint is welcome. > > Thanks and kind regards, > > Mike > > >> sessionInfo() > R version 2.11.1 (2010-05-31) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] crlmm_1.6.5 oligoClasses_1.10.0 Biobase_2.8.0 > [4] ff_2.1-2 bit_1.1-4 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 > [4] Biostrings_2.16.9 DBI_0.2-5 ellipse_0.3-5 > [7] genefilter_1.30.0 IRanges_1.6.16 mvtnorm_0.9-92 > [10] preprocessCore_1.10.0 RSQLite_0.9-2 splines_2.11.1 > [13] survival_2.35-8?????? xtable_1.5-6 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD REPLYlink written 8.7 years ago by Matthew Ritchie750
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