Re: [aroma.affymetrix] AffymetrixCdfFile$byChipType -- Argument 'nbrOfUnits' contains 1 NA value(s)
Dear Guido,
Thank you for your reply, I followed your much simpler code and it worked!
So it seems I got mixed up with the folders. Or it could be that I should
have set the working directory with setwd(). I think I assumed that
aroma.affymetrix would use the wd variable to find the appropriate files. I
was surprised it didn't say that it couldn't locate the file as in other
posts in the mailing list.
In any case, it works now!
Thanks for your help,
Best wishes,
Sophie.
Code that worked:
setwd("~/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd")
library(aroma.affymetrix)
chipType <- "RaGene-2_1-st"
cdf <- AffymetrixCdfFile$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_0.1-3aroma.apd_0.6.0R.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=qFHaMnoJ
>
> http://www.researcherid.com/rid/F-4912-2010
>
>
>
> *From:* aroma-a
RE: [aroma.affymetrix] AffymetrixCdfFile$byChipType -- Argument 'nbrOfUnits' contains 1 NA value(s)
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_3.3.1R.cache_0.12.0
parallel_3.3.1
[11] base64enc_0.1-3aroma.apd_0.6.0R.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=qFHaMnoJ
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$byChipType.
I've set up the folders and files as advised, and got the cdf file for
RaGene-2_1-st from http://nmg-r.bioinformatics.nl/NuGO_R.html.
My command to create the cdf object fails with the error (detailed below):
Argument 'nbrOfUnits' contains 1 NA value(s).
Would you have any suggestion of what I'm doing wrong?
Thanks very much for your help,
Best wishes,
Sophie.
Here is my code:
require(aroma.affymetrix)
require(biomaRt)
require(GenomeGraphs)
wd <-
"/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd"
ds <- "myDataSet"
cel.directory <-
"/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd/rawData/myDataSet/RaGene-2_1-st"
annotation.data<-"/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd/annotationData/chipTypes/RaGene-2_1-st"
output.folder <-
"/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd/output"
library.file
<-"/Users/sdeproce/Documents/AITMAN_GROUP/KO_SHR_rat_strains/Transcriptomes/aroma_affymetrix_wd/annotationData/chipTypes/RaGene-2_1-st/RaGene-2_1-st,byTranscript-fsetid,pd.ragene.2.1.st.cdf"
chipType<-"
[aroma.affymetrix] AffymetrixCdfFile$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 '' 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 '' 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_1.34.0biomaRt_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_1.10.3XVector_0.14.1 bitops_1.0-6 base64enc_0.1-3tools_3.3.2 zlibbioc_1.20.0digest_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_0.20.0GenomicRanges_1.26.4 SummarizedExperiment_1.4.0 future_1.4.0 R.huge_0.9.0
