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

[Shu-wen Huang]

I tried to use rma() shown below. However, it seems I can't go around the need of sorghwta520972fcdf. Or did I misunderstand what you suggested?

>eset = rma(dat)

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


Sw


-----Original Message-----
From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com] 
Sent: Saturday, April 14, 2012 8:08 PM
To: Shu-wen Huang
Cc: bioconductor at r-project.org
Subject: Re: [BioC] How to generate an annotation library without CDF file?

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/do
>> c
>> /primer.pdf
>>
>> benilton