Entering edit mode
Guido Hooiveld
★
4.1k
@guido-hooiveld-2020
Last seen 19 hours ago
Wageningen University, Wageningen, the …
Dear list,
I am using Affxparser to create/save CEL files from an AffyBatch
object.
The code I use used to work fine before 2 yrs ago, but now I get a
warning. Although the corresponding CDF file is installed, and the new
CEL file is properly created, I would appreciate getting feedback how
to
avoid this warning. Code below.
Thanks,
Guido
> library(affxparser)
> library(affy)
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Warning message:
package 'affy' was built under R version 2.9.1
> affy.data <- ReadAffy()
> affy.data
AffyBatch object
size of arrays=712x712 features (11 kb)
cdf=ATH1-121501 (22810 affyids)
number of samples=24
number of genes=22810
annotation=ath1121501
notes=
>
> prefix <- "Guido"
>
> #get the intensity
> size = ncol(affy.data)
> IN = intensity(affy.data)
>
> #get the celfile names
> cels = colnames(IN)
> #put the prefix to the celfile names
> newcels = paste(prefix,cels,sep="-")
> #get the number of chips
> col.count = dim(IN)[2]
> #go through each chip and write the new celfile for it
> for( i in 1:col.count){
+ #old celfile name for this chip
+ file.name = cels[i]
+ #new celfile name for this chip
+ file.name2 = newcels[i]
+ INi <- IN[,i];
+ INi[is.na(INi)] = 1000000000;
+ meg = paste("handling file:",file.name)
+ print (meg)
+
+ # Read the CEL header
+ HDRi <- readCelHeaderfile.name)
+ HDRi$chiptype <- cleancdfname(HDRi$chiptype,
addcdf=FALSE)
+
+ # Create a CEL v4 file of the same chip type
+ outFile <- file.path(as.character(file.name2))
+ if (file.exists(outFile))
+ file.remove(outFile)
+ createCel(outFile, HDRi, overwrite=TRUE)
+
+ # Update the newly created CEL file by injecting corrected values
+ updateCel(outFile, indices=NULL, intensities=INi)
+ }
[1] "handling file: A175_11_WT.CEL"
[1] "handling file: A175_12_WT.CEL"
[1] "handling file: A175_13_WT.CEL"
[1] "handling file: A175_21_S036.CEL"
<snip>
[1] "handling file: A175_82_OXS042.CEL"
[1] "handling file: A175_83_OXS042.CEL"
There were 24 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In createCel(outFile, HDRi, overwrite = TRUE) :
Skipping validation of CEL header against CDF header. Could not find
a
CDF file for this chip type: ath1121501
2: In createCel(outFile, HDRi, overwrite = TRUE) :
Skipping validation of CEL header against CDF header. Could not find
a
CDF file for this chip type: ath1121501
3: In createCel(outFile, HDRi, overwrite = TRUE) :
Skipping validation of CEL header against CDF header. Could not find
a
CDF file for this chip type: ath1121501
4: In createCel(outFile, HDRi, overwrite = TRUE) :
Skipping validation of CEL header against CDF header. Could not find
a
CDF file for this chip type: ath1121501
<and 20="" additional,="" identical="" warnings)=""> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ath1121501cdf_2.4.0 affy_1.22.1 Biobase_2.4.1
affxparser_1.16.0
loaded via a namespace (and not attached):
[1] affyio_1.12.0 preprocessCore_1.6.0 tools_2.9.0
>
------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/>
email: guido.hooiveld@wur.nl
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