[BioC] inquiry for CDF file

[Rob Dunne]

Hi Benilton,

yes, version 1.5.2  (and an upgrade of oligo and oligoClasses) fixed the 
problem.
However the function "readPgfEnv" is not found

Bye
Rob



library(pdInfoBuilder)
pgfFile <- "RaGene-1_0-st-v1.r3.pgf"
clfFile <- "RaGene-1_0-st-v1.r3.clf"
transFile <- " RaGene-1_0-st-v1.na25.rn4.transcript.csv"
probeFile <- "RaGene-1_0-st-v1.probe.tab"
pkg <- new("AffyGenePDInfoPkgSeed", author = "Rob Dunne", email =
"rob.dunne at csiro.au", version = "0.0.1", genomebuild = "Fri Sep 26 
19:30:54 2008",
biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile,
transFile = transFile, probeFile = probeFile)
makePdInfoPackage(pkg)
#Error in chipName(object) : could not find function "readPgfEnv"



Benilton Carvalho wrote:
> If you could, please, try version 1.5.2 (devel) and report back with 
> your findings, I'd very much appreciate.
>
> http://www.bioconductor.org/packages/2.3/bioc/html/pdInfoBuilder.html
>
> best,
>
> b
>
> On Sep 28, 2008, at 9:48 PM, Rob Dunne wrote:
>
>> HI List,
>> I get the error message
>>
>>  "AffyGenePDInfoPkgSeed" is not a defined class
>>
>> when I try to use pdInfoBuilder, but this posted example seems to
>> indicate it works for some.
>>
>> James W. MacDonald wrote:
>>
>>> You then have to create a 'AffyGenePDInfoPkgSeed' object which you can
>>> then use to build the package. The help page for this doesn't really
>>> cover this sort of thing, so here is an example of how you would do so:
>>>
>>> pgfFile <- "MoGene-1_0-st-v1.r3.pgf"
>>> clfFile <- "MoGene-1_0-st-v1.r3.clf"
>>> transFile <- "MoGene-1_0-st-v1.na24.mm8.transcript.csv"
>>> probeFile <- "MoGene-1_0-st-v1.probe.tab"
>>>
>>> pkg <- new("AffyGenePDInfoPkgSeed", author = "authorname", email =
>>> "e at mail.net", version = "0.0.1", genomebuild = "thegenomebuilddate",
>>> biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile,
>>> transFile = transFile, probeFile = probeFile)
>>>
>>> makePdInfoPackage(pkg)
>>
>> library(pdInfoBuilder)
>> pgfFile <- "RaGene-1_0-st-v1.r3.pgf"
>> clfFile <- "RaGene-1_0-st-v1.r3.clf"
>> transFile <- " RaGene-1_0-st-v1.na25.rn4.transcript.csv"
>> probeFile <- "RaGene-1_0-st-v1.probe.tab"
>>
>>
>>
>> pkg <- new("AffyGenePDInfoPkgSeed", author = "Rob Dunne", email =
>> "rob.dunne at csiro.au", version = "0.0.1", genomebuild = "Fri Sep 26
>> 19:30:54 2008",
>> biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile,
>> transFile = transFile, probeFile = probeFile)
>> #Error in getClass(Class, where = topenv(parent.frame())) :
>> #  "AffyGenePDInfoPkgSeed" is not a defined class
>>
>> pdInfoBuilder is the current version (1.2.0) and R is 2.6.2
>>
>> Bye
>> Rob
>>
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>


-- 
Rob Dunne         Fax: +61 2 9325 3200     Tel: +61 2 9325 3263
CSIRO Mathematical and Information Sciences     +61 2 9325 3100
Locked Bag 17, North Ryde, New South Wales, Australia, 1670
http://www.bioinformatics.csiro.au Email: Rob.Dunne at csiro.au

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