[BioC] HuGene-1_0-st-v1.r4.pgf

[Martin Morgan]

Oops, cut and paste incorrect below, I meant

> library(AffyCompatible)
> rsrc <- NetAffxResource(user="mtmorgan at fhcrc.org", password=password)
> names(rsrc)
[SNIP]
[53] "HuEx-1_0-st-v2"                 "HuGene-1_0-st-v1"
...
> names(rsrc[["HuGene-1_0-st-v1"]])
 [1] "Probe Sequences, FASTA format"
 [2] "Probe Sequences, tabular format"
 [3] "Probeset Annotations, CSV Format"
 [4] "Transcript Cluster Annotations, CSV"
 [5] "Transcript Cluster Sequences, FASTA format"
 [6] "BED File"
 [7] "Background Probes File"
 [8] "Intensity Layout File"
 [9] "EC Default Analysis Specifications"
 [10] "Meta Probeset File"
 [11] "Probe Group File"
 [12] "Probeset List File"
 [13] "QC Control File"
> pgf <- rsrc[["HuGene-1_0-st-v1", "Probe Group File"]]
> affxUrl(affxFile(pgf)[[1]])[[1]]
.Data:
http://www.affymetrix.com/analysis/downloads/na27/wtgene/HuGene-1_0-st-v1.r4.pgf.zip
affxCompression: application/zip
affxCrc32:
affxSize: 14242053
 

Martin Morgan <mtmorgan at fhcrc.org> writes:

> Hi Mayte --
>
> Here's a different way to find things, see the 'Annotation Retrieval
> with NetAffx' vignette in the AffyCompatible package for more details
>
>> library(AffyCompatible)
>> rsrc <- NetAffxResource(user="mtmorgan at fhcrc.org", password=password)
>> pgf
> affxType: pgf
> affxDescription: Probe Group File
> affxFile: AffxFile(1)
>> affxUrl(affxFile(pgf)[[1]])[[1]]
> .Data:
> http://www.affymetrix.com/analysis/downloads/na27/wtgene/HuGene-1_0-st-v1.r4.pgf.zip
> affxCompression: application/zip
> affxCrc32:
> affxSize: 14242053
>
> Martin
>
>
> Mayte Suarez-Farinas wrote:
>> Hi,
>> I am trying to use xps to work with HuGene 1.0
>> I have already ROOT and xps and I am following
>> their code to create the root scheme. The use of this packages are
>> more laborious that the annotation "ways' for other affychip,
>> but I am doing by best. For what I understand
>> I have to download  HuGene-1_0-st-v1.r4.clf,HuGene-1_0-st- 
>> v1.na28.hg18.transcript.csv
>> and  HuGene-1_0-st-v1.r4.pgf form Affywebsite. I was able to find the  
>> first two but not the
>> last one. ie: HuGene-1_0-st-v1.r4.pgf
>> 
>> any help??
>> 
>> 
>> scheme.hugene10stv1r3.na27 <- import.genome.scheme 
>> ("Scheme_HuGene10stv1r4_na28",filedir=scmdir,
>>                                paste(libdir,"HuGene-1_0-st- 
>> v1.r4.clf",sep="/"),
>>                                paste(libdir,"HuGene-1_0-st- 
>> v1.r4.pgf",sep="/"),
>>                                paste(anndir,"HuGene-1_0-st- 
>> v1.na28.hg18.transcript.csv",sep="/"))
>> 
>> Mayte
>> 	[[alternative HTML version deleted]]
>> 
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>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109

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