AffymetrixCdfFile$byChipType -- Argument 'nbrOfUnits' contains 1 NA value(s)

Sophie Marion de Procé

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Apr 3, 2017, 1:09:48 PM4/3/17

to aroma.affymetrix

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

Hooiveld, Guido

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Apr 5, 2017, 3:48:41 AM4/5/17

to aroma.affymetrix

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.h...@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

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Sophie Marion de Procé

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Apr 5, 2017, 5:41:56 AM4/5/17

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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"))

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