Hi, Creating the CDF object using the same binary CDF file works fine in my hands… ?? See below.
It has been a while since I extensively used aroma.affymetrix, but I noticed the main difference between your and my code is that you specifically set in R all relevant directories (cel.directory, annotation.data, etc), whereas I just set the working directory (to “aroma.affy.test”). That was the only directory I set/specified. Before starting R/aroma.affymetrix I downloaded the binary CDF file, and within this (working) directory I created the relevant CDF directory (i.e. D:\aroma.affy.test\annotationData\chipTypes\RaGene-2_1-st), and then copied the CDF into that dir. Next I ran the code below. Note that I am on a Windows machine. Also note that since I don’t have some RaGene 2.1 CEL files I could not test whether the subsequent normalization goes fine. HTH, Guido > setwd("D:\\aroma.affy.test") > > library(aroma.affymetrix) > chipType <- "RaGene-2_1-st" > cdf <- AffymetrixCdfFile$byChipType(chipType, tags=c("byTranscript-fsetid", > "pd.ragene.2.1.st")) > print(cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/RaGene-2_1-st Filename: RaGene-2_1-st,byTranscript-fsetid,pd.ragene.2.1.st.cdf File size: 15.00 MiB (15728222 bytes) Chip type: RaGene-2_1-st,byTranscript-fsetid,pd.ragene.2.1.st File format: v4 (binary; XDA) Dimension: 1190x1190 Number of cells: 1416100 Number of units: 36685 Cells per unit: 38.60 Number of QC units: 0 > > > sessionInfo() R version 3.3.1 Patched (2016-10-18 r71535) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aroma.light_3.4.0 aroma.affymetrix_3.1.0 affxparser_1.46.0 aroma.core_3.1.0 [5] R.devices_2.15.1 R.filesets_2.11.0 R.utils_2.5.0 R.oo_1.21.0 [9] R.methodsS3_1.7.1 loaded via a namespace (and not attached): [1] matrixStats_0.52.0 codetools_0.2-15 listenv_0.6.0 future_1.4.0 digest_0.6.12 [6] R.huge_0.9.0 PSCBS_0.62.0 tools_3.3.1 R.cache_0.12.0 parallel_3.3.1 [11] base64enc_0.1-3 aroma.apd_0.6.0 R.rsp_0.40.0 globals_0.9.0 DNAcopy_1.48.0 > --------------------------------------------------------- Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition & Health Wageningen University Visiting address: Mail address: HELIX (Building 124), room 2048 Stippeneng 4 PO Box 17 6708 WE Wageningen 6700 AA Wageningen the Netherlands the Netherlands tel: (+) 31 317 485788 fax: (+) 31 317 483342 email: guido.hooiv...@wur.nl internet: http://www.wur.nl/nmg/hooiveld internet: http://www.wur.nl/nmg http://scholar.google.com/citations?user=qFHaMnoAAAAJ http://www.researcherid.com/rid/F-4912-2010 From: aroma-affymetrix@googlegroups.com [mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Sophie Marion de Procé Sent: Monday, April 03, 2017 18:15 To: aroma.affymetrix <aroma-affymetrix@googlegroups.com> Subject: [aroma.affymetrix] AffymetrixCdfFile$byChipType -- Argument 'nbrOfUnits' contains 1 NA value(s) Dear all, I'm new to aroma.affymetrix and I seem to be stuck at the cdf file step using AffymetrixCdfFile$byChipType. I've set up the folders and files as advised, and got the cdf file for RaGene-2_1-st from http://nmg-r.bioinformatics.nl/NuGO_R.html. My command to create the cdf object fails with the error (detailed below): Argument 'nbrOfUnits' contains 1 NA value(s). Would you have any suggestion of what I'm doing wrong? Thanks very much for your help, Best wishes, Sophie. Here is my code: require(aroma.affymetrix) require(biomaRt) require(GenomeGraphs) wd <- "/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd" ds <- "myDataSet" cel.directory <- "/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd/rawData/myDataSet/RaGene-2_1-st" annotation.data<-"/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd/annotationData/chipTypes/RaGene-2_1-st" output.folder <- "/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd/output" library.file <-"/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd/annotationData/chipTypes/RaGene-2_1-st/RaGene-2_1-st,byTranscript-fsetid,pd.ragene.2.1.st.cdf" chipType<-"RaGene-2_1-st" sample.info <-read.table(file=paste(cel.directory,"SampleInformation.txt", sep="/"),sep="\t", header=TRUE) transcript.clusters.NetAffx.36 <- read.csv(file=paste(annotation.data,"RaGene-2_1-st-v1.na36.rn5.transcript.csv",sep="/"), skip=22) probesets.NetAffx.36 <-read.csv(file=paste(annotation.data,"RaGene-2_1-st-v1.na36.rn5.probeset.csv",sep ="/"), skip=21) cdf <- AffymetrixCdfFile$byChipType(chipType,tags="byTranscript-fsetid","pd.ragene.2.1.st") # FAILS And the error message I get: [2017-04-03 17:02:35] Exception: Argument 'nbrOfUnits' contains 1 NA value(s). at #10. getNumerics.Arguments(static, ..., asMode = "integer", disallow = disallow) - getNumerics.Arguments() is in environment 'R.utils' at #09. getNumerics(static, ..., asMode = "integer", disallow = disallow) - getNumerics() is in environment 'R.utils' at #08. getIntegers.Arguments(static, ..., length = length) - getIntegers.Arguments() is in environment 'R.utils' at #07. getIntegers(static, ..., length = length) - getIntegers() is in environment 'R.utils' at #06. getInteger.Arguments(static, ...) - getInteger.Arguments() is in environment 'R.utils' at #05. getInteger(static, ...) - getInteger() is in environment 'R.utils' - originating from '<text>' at #04. Arguments$getInteger(nbrOfUnits, range = c(0, Inf)) - Arguments$getInteger() is local of the calling function at #03. byChipType.UnitAnnotationDataFile(static, ...) - byChipType.UnitAnnotationDataFile() is in environment 'aroma.core' at #02. byChipType(static, ...) - byChipType() is in environment 'aroma.core' - originating from '<text>' at #01. AffymetrixCdfFile$byChipType(chipType, tags = "byTranscript-fsetid", "pd.ragene.2.1.st") - AffymetrixCdfFile$byChipType() is local of the calling function Error: Argument 'nbrOfUnits' contains 1 NA value(s). In addition: Warning message: In storage.mode(x) <- asMode : NAs introduced by coercion Finally, my sessionInfo(): R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X El Capitan 10.11.6 locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] GenomeGraphs_1.34.0 biomaRt_2.30.0 aroma.light_3.4.0 aroma.affymetrix_3.1.0 aroma.core_3.1.0 R.devices_2.15.1 R.filesets_2.11.0 R.utils_2.5.0 R.oo_1.21.0 affxparser_1.46.0 R.methodsS3_1.7.1 loaded via a namespace (and not attached): [1] Rcpp_0.12.10 GenomeInfoDb_1.10.3 XVector_0.14.1 bitops_1.0-6 base64enc_0.1-3 tools_3.3.2 zlibbioc_1.20.0 digest_0.6.12 aroma.apd_0.6.0 [10] memoise_1.0.0 RSQLite_1.1-2 lattice_0.20-35 R.cache_0.12.0 Matrix_1.2-8 DBI_0.6 parallel_3.3.2 R.rsp_0.40.0 S4Vectors_0.12.2 [19] PSCBS_0.62.0 globals_0.9.0 IRanges_2.8.2 stats4_3.3.2 Biobase_2.34.0 listenv_0.6.0 DNAcopy_1.48.0 AnnotationDbi_1.36.2 XML_3.98-1.6 [28] codetools_0.2-15 matrixStats_0.51.0 BiocGenerics_0.20.0 GenomicRanges_1.26.4 SummarizedExperiment_1.4.0 future_1.4.0 R.huge_0.9.0 RCurl_1.95-4.8 Cairo_1.5-9 -- -- 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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