[BioC] Cannot find MoGene-1.0

[Manhong Dai]

Hi Peter,


	This chip is supported in Custom CDF version 11, you can google 'custom
cdf' for detail.


Best,
Manhong
> Date: Sun, 01 Mar 2009 11:14:50 +0100
> From: Peter Robinson <peter.robinson at t-online.de>
> Subject: [BioC] Cannot find MoGene-1.0
> To: Bioconductor at stat.math.ethz.ch
> Message-ID: <49AA601A.90204 at t-online.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi all,
> 
> I am trying to use the affy package to analyze  GeneChip? Mouse Gene 1.0 
> ST Array data.  What do I need to do to get the CDF information for this 
> chip? I am loading the
> mogene10st.db package, but that doesnt seem to be correct.
> Thanks a lot, Peter
> 
>  > library(affy)
> Lade n?tiges Paket: Biobase
> Lade n?tiges Paket: tools
> 
> Welcome to Bioconductor
> 
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
> 
> Lade n?tiges Paket: affyio
> Lade n?tiges Paket: preprocessCore
> 
>  > library(mogene10st.db)
> Lade n?tiges Paket: AnnotationDbi
> Lade n?tiges Paket: DBI
>  > myAffy = ReadAffy(filenames=celfiles)
> 
>  > myAffy
> AffyBatch object
> size of arrays=1050x1050 features (11 kb)
> cdf=MoGene-1_0-st-v1 (??? affyids)
> number of samples=24
> Fehler in getCdfInfo(object) :
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain MoGene-1_0-st-v1
> Library - package mogene10stv1cdf not installed
> Data for package affy did not contain mogene10stv1cdf
> Bioconductor - mogene10stv1cdf not available
> Zus?tzlich: Warning message:
> missing cdf environment! in show(AffyBatch)
> 
> 
>  > sessionInfo()
> R version 2.8.1 (2008-12-22)
> i486-pc-linux-gnu
> 
> locale:
> LC_CTYPE=de_DE at euro;LC_NUMERIC=C;LC_TIME=de_DE at euro;LC_COLLATE=de_DE at euro;LC_MONETARY=C;LC_MESSAGES=de_DE at euro;LC_PAPER=de_DE at euro;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE at euro;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
> 
> other attached packages:
> [1] mogene10st.db_1.0.2  RSQLite_0.6-4        DBI_0.2-4
> [4] AnnotationDbi_1.4.3  affy_1.18.2          preprocessCore_1.2.0
> [7] affyio_1.8.0         Biobase_2.0.1
>