[BioC] Affxparser: how to create CEL-file from AffyBatch
James W. MacDonald
jmacdon at med.umich.edu
Wed Jul 2 22:36:30 CEST 2008
Hi Guido,
Hooiveld, Guido wrote:
> Dear list,
>
> My basic understanding of R/BioC doesn't allow me to solve my problem,
> so I hope someone can point me to the right direction.
>
> Basically, my question is how to extract/create/save the data embedded
> in an AffyBatch object as individual *.CEL files (using Affxparser).
>
> -->
> I am using HarshLight to 'correct' a bunch of CEL files (12x MOE430A
> arrays) for blemish. Running HarshLight goes fine, but I then would like
> to save the corrected files (as *.CEL) to my HDD.
> A function called 'Helpers' (available @ the site of the Harslight
> developers) normally used for this, doesn't work for me... See below for
> error (I will also directly contact the authors about this).
>
> Hinted by a recent thread, I tried to give Afxxparser a try. Main reason
> for this is that this likely is a more generic way of saving CEL files
> from an AffyBatch object than using 'Helpers'.
>
> http://article.gmane.org/gmane.science.biology.informatics.conductor/184
> 55
> <cut/paste>
> From: James W. MacDonald <jmacdon at ...>
> Subject: Re: AffyBatch -> CEL File
> Newsgroups: gmane.science.biology.informatics.conductor
> Date: 2008-06-16 14:18:16 GMT
> Hi Markus,
>
> Markus Schmidberger wrote:
>
>> Hello,
>>
>> is there any function or package to create a CEL File (or CEL files)
>> from an AffyBatch?
>>
> Seems to me you could use createCel() and updateCel() from the
> affxparser package.
>
> Best,
> Jim
> </cut/paste>
>
>
>
> But now I am getting lost....
> AFter checking the Affxparser help pages I tried this:
>
> # Note: next 4 lines directly copied from help pages Affxparser:
>
>> celFiles <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
>> if (length(celFiles) == 0)
>>
> + break;
>
>> celFile <- celFiles[1]
>> celFile
>>
> [1] "A23_mIntestine_KOWY7.CEL"
>
> # usage createCel should be: "createCel(outFile, hdr, overwrite=TRUE)"
>
>> hdr <- readCelHeader(celFile)
>> createCel("celGuido.CEL", hdr, overwrite=TRUE)
>>
> Warning message:
> In createCel("celGuido.CEL", hdr, overwrite = TRUE) :
> Could not find a CDF file for this chip type: MOE430A
>
>> traceback()
>>
> No traceback available
>
>
> In other words, I cannot get the first step to work [createCel()]....
> let alone the 2nd [updateCel()]
>
Where exactly is the error? I see a warning that you don't have the CDF
file, and I assume you know how to get that. But a warning is not an
error, so what exactly is the problem?
>
> Therefore, to get me further, I would appreciate if someone could
> provide some lines of code on how to extract/save multiple CEL files
> from an AffyBatch object.
>
> Many thanks in advance,
> Guido
>
>
>
> HarshLight:
> http://www.bioconductor.org/packages/2.2/bioc/html/Harshlight.html
> For 'Helpers':
> http://asterion.rockefeller.edu/Harshlight/index2.html
>
> Full Code:
> library(affy)
> library(Harshlight)
> library(Helpers)
> library(affxparser)
>
> data <- ReadAffy()
>
>
>> data
>>
> AffyBatch object
> size of arrays=712x712 features (9 kb)
> cdf=MOE430A (22690 affyids)
> number of samples=12
> number of genes=22690
> annotation=moe430a
> notes=
>
>> ab <- Harshlight(data, na.sub = FALSE)
>>
> [1] "Generating Error Images"
> [1] "Initializing Harshlight"
> [1] "Analyzing chip number 1"
> [1] "Analyzing chip number 2"
> [1] "Analyzing chip number 3"
> [1] "Analyzing chip number 4"
> [1] "Analyzing chip number 5"
> [1] "Analyzing chip number 6"
> [1] "Analyzing chip number 7"
> [1] "Analyzing chip number 8"
> [1] "Analyzing chip number 9"
> [1] "Analyzing chip number 10"
> [1] "Analyzing chip number 11"
> [1] "Analyzing chip number 12"
> [1] "Substituting values"
>
>
>> ab
>>
> AffyBatch object
> size of arrays=712x712 features (9 kb)
> cdf=MOE430A (22690 affyids)
> number of samples=12
> number of genes=22690
> annotation=moe430a
> notes=
>
>
>> library(Helpers)
>> WriteAbatch(ab,prefix="hl")
>>
> [1] "handling file: A23_mIntestine_KOWY7.CEL"
> The file does not look like a CEL file in TXT format.
> End of file reached unexpectedly. Perhaps this file is truncated.
> [1] "An error occurre while trying to write to:
> hl-A23_mIntestine_KOWY7.CEL"
> [1] "handling file: A23_mIntestine_KOWY8.CEL"
> The file does not look like a CEL file in TXT format.
> # <snip>; the same error for all 12 arrays
>
> I then continued with using Affxparser as described above.
>
>
>
>> sessionInfo()
>>
> R version 2.7.0 (2008-04-22)
> 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] tools stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] Helpers_0.2-1 affydata_1.11.3 Biobase_2.0.1
> affxparser_1.12.2 Harshlight_1.10.0
> [6] altcdfenvs_2.2.0 hypergraph_1.12.0 graph_1.18.1
> Biostrings_2.8.4 makecdfenv_1.18.0
> [11] matchprobes_1.12.0 affy_1.18.0 preprocessCore_1.2.0
> affyio_1.8.0
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.10
>
>
>
>
>
> ------------------------------------------------
> 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 at wur.nl
>
>
>
> [[alternative HTML version deleted]]
>
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