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: [email protected]
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: [email protected]
[mailto:[email protected]] On Behalf Of Sophie Marion de Procé
Sent: Monday, April 03, 2017 18:15
To: aroma.affymetrix <[email protected]>
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
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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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