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


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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.


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