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

[Benilton Carvalho]

You did misunderstand.

1) Get all your files
2) Install the pdInfoBuilder package
3) Use the example in Section 8 of the pdInfoBuilder vignette (
http://bioconductor.org/packages/release/bioc/vignettes/pdInfoBuilder/inst/doc/BuildingPDInfoPkgs.pdf
)
4) Install the resulting annotation package
5) Install oligo
6) Use the Sections 1 and 4 of the document I suggested on my first message.

b

On 15 April 2012 02:16, Shu-wen Huang <shuang at chromatininc.com> wrote:
> 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