[BioC] How to generate an annotation library without CDF file?

[Benilton Carvalho]

With the files you current have, you could generate the appropriate
annotation package and work with the preprocessing steps through oligo
and shown on the sections of the document I suggested initially.
However, I'm not sure gcrma() would work with oligo objects - in the
meantime, you could use rma(). Maybe Jean can provide further
insight...

b

On 15 April 2012 01:55, Shu-wen Huang <shuang at chromatininc.com> wrote:
> Below are my codes. It seems I need to somehow generate Sorgh-WTa520972F Library in order to do Normalization. However, I don't have CDF file, but many other format files.
>
>
>>library(affy)
>>library(limma)
>>library(gcrma)
>>library(genefilter)
>
> ## read the Targets.txt file ##
>>setwd("all")
>>targets = readTargets()
>
> ## create a phenodata object and attach it to the data ##
>>myCovs = data.frame(targets)
>>rownames(myCovs) = myCovs[,1]
>>nlev = as.numeric(apply(myCovs, 2, function(x) nlevels(as.factor(x))))
>>metadata = data.frame(labelDescription = paste(colnames(myCovs), ": ", nlev, " level", ifelse(nlev==1,"","s"), sep=""), >row.names=colnames(myCovs))
>>phenoData = new("AnnotatedDataFrame", data=myCovs, varMetadata=metadata)
>
> ## read the data, attach the phenodata and normalize it using gcRMA ##
>>dat = ReadAffy(sampleNames = myCovs$Name, filenames = myCovs$Celfile, phenoData = phenoData, celfile.path = "celfiles")
>>eset = gcrma(dat, verbose = FALSE)
>
>
>
> ############ error messages received ############
> Error in getCdfInfo(object) :
>  Could not obtain CDF environment, problems encountered:
> Specified environment does not contain Sorgh-WTa520972F
> Library - package sorghwta520972fcdf not installed
> Bioconductor - sorghwta520972fcdf not available
>
>
>
>
>
> -----Original Message-----
> From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com]
> Sent: Saturday, April 14, 2012 7:48 PM
> To: Shu-wen Huang
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] How to generate an annotation library without CDF file?
>
> To generate an annotation package, you should use the PGF file... and one alternative for this is the pdInfoBuilder package... but without further details, it's hard to go on...
>
> benilton
>
> On 15 April 2012 01:40, Shu-wen Huang <shuang at chromatininc.com> wrote:
>> Hi benilton,
>>
>> Our group generated a particular list of probes. It's not available in BioConductor. Do you mean I should try to generate a library from PGF file? Thanks!
>>
>>
>> Sw
>>
>> -----Original Message-----
>> From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com]
>> Sent: Saturday, April 14, 2012 6:29 PM
>> To: Shu-wen Huang
>> Cc: bioconductor at r-project.org
>> Subject: Re: [BioC] How to generate an annotation library without CDF file?
>>
>> PGFs are given for Gene/Exon ST arrays... and chances are that the
>> package you need is already on BioConductor. (btw, a CDF for such
>> array design is not recommended by Affymetrix themselves)
>>
>> Check Sections 1 and 4 of the document below:
>>
>> http://bioconductor.org/packages/release/bioc/vignettes/oligo/inst/doc
>> /primer.pdf
>>
>> benilton