[BioC] inquiry for CDF file

[James W. MacDonald]

Rob Dunne wrote:
> Hi Benilton,
> 
> yes, version 1.5.2  (and an upgrade of oligo and oligoClasses) fixed the 
> problem.
> However the function "readPgfEnv" is not found

Did you upgrade to R-devel, or simply install the devel version of 
pdInfoBuilder in your R-2.6.2 installation?

> 
> 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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>>
> 
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662