Dear Guido,
Thank you for your reply, I followed your much simpler code and it worked!
So it seems I got mixed up with the folders. Or it could be that I should
have set the working directory with setwd(). I think I assumed that
aroma.affymetrix would use the wd variable to find the appropriate files. I
was surprised it didn't say that it couldn't locate the file as in other
posts in the mailing list.
In any case, it works now!
Thanks for your help,
Best wishes,
Sophie.
Code that worked:
setwd("~/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd")
library(aroma.affymetrix)
chipType <- "RaGene-2_1-st"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags=c("byTranscript-fsetid",
"pd.ragene.2.1.st"))
On 5 April 2017 at 08:48, Hooiveld, Guido <guido.hooiv...@wur.nl> wrote:
> Hi,
>
> Creating the CDF object using the same binary CDF file works fine in my
> hands… ?? See below.
>
>
>
> It has been a while since I extensively used aroma.affymetrix, but I
> noticed the main difference between your and my code is that you
> specifically set in R all relevant directories (cel.directory,
> annotation.data, etc), whereas I just set the working directory (to
> “aroma.affy.test”). That was the only directory I set/specified.
>
>
>
> Before starting R/aroma.affymetrix I downloaded the binary CDF file, and
> within this (working) directory I created the relevant CDF directory (i.e.
> D:\aroma.affy.test\annotationData\chipTypes\RaGene-2_1-st), and then
> copied the CDF into that dir.
>
> Next I ran the code below.
>
>
>
> Note that I am on a Windows machine. Also note that since I don’t have
> some RaGene 2.1 CEL files I could not test whether the subsequent
> normalization goes fine.
>
>
>
> HTH,
>
> Guido
>
>
>
> > setwd("D:\\aroma.affy.test")
>
> >
>
> > library(aroma.affymetrix)
>
> > chipType <- "RaGene-2_1-st"
>
> > cdf <- AffymetrixCdfFile$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 <+31%20317%20485%20788>
>
> fax: (+) 31 317 483342 <+31%20317%20483%20342>
>
> 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.
>
>
> You received this message because you are subscribed to the Google Groups
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> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/
> forum/
>
> ---
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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
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/
> forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
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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
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
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To unsubscribe and other options, go to http://www.aroma-project.org/forum/
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