[BioC] verification

[Vasiliki Xiarchou]

bioconductor-request at stat.math.ethz.ch wrote:
> Send Bioconductor mailing list submissions to
> 	bioconductor at stat.math.ethz.ch
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://stat.ethz.ch/mailman/listinfo/bioconductor
> or, via email, send a message with subject or body 'help' to
> 	bioconductor-request at stat.math.ethz.ch
>
> You can reach the person managing the list at
> 	bioconductor-owner at stat.math.ethz.ch
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bioconductor digest..."
>
>
> Today's Topics:
>
>    1. Re: crlmm warning (Morten Mattingsdal)
>    2. Re: crlmm warning (James W. MacDonald)
>    3. Re: crlmm warning (Benilton Carvalho)
>    4. Re: crlmm warning (Morten Mattingsdal)
>    5. Re: Unable to compile the impute package on debian with gcc
>       4.1 (Seth Falcon)
>    6. Re: rma on new samples (Hassane, Duane)
>    7. Re: crlmm warning (Benilton Carvalho)
>    8. NEwbie: How to determine significant enrichment differences
>       of GO term vectors? (Johannes Graumann)
>    9. Re: rma on new samples (Kuhn, Max)
>   10. Options for spatial normalization? (Oliver Homann)
>   11. how to enlarge memory (Yihuan Xu)
>   12. Re: how to enlarge memory (James W. MacDonald)
>   13. Re: Options for spatial normalization? (Jay Konieczka)
>   14. RMA, RefRMA questions (James Anderson)
>   15. Re: RMA, RefRMA questions (Kuhn, Max)
>   16. Re: RMA, RefRMA questions (James W. MacDonald)
>   17. Re: RMA, RefRMA questions (Kuhn, Max)
>   18. two questions about limma (cont.2) (De-Jian,ZHAO)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 07 Mar 2007 13:10:59 +0100
> From: Morten Mattingsdal <mortenm at inbox.com>
> Subject: Re: [BioC] crlmm warning
> To: Morten Mattingsdal <mortenm at inbox.com>
> Cc: BioC <bioconductor at stat.math.ethz.ch>
> Message-ID: <45EEABD3.70208 at inbox.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello again,
> Ill just answer that myself, since I posted a bit too prematurely.
> Seems like I need to use the makePlatformDesign package, with the code:
>
>  > library(makePlatformDesign)
>  > 
> makePDpackage("Mapping50K_Xba240.CDF","Mapping50K_Xba240_probe_fasta","Mapping50K_Xba240_annot.csv",type="SNP")
>
> R CMD INSTALL pdmapping50kxba240
>
> I find it ... non-trivial.. to locate the fasta file for Nsp and Sty 
> arrays, but I think Ill harass Affyemtrix Inc for that.
>
> I am aware that the oligo package is in development, but It would be 
> nice to have some vignettes to read
>
> regards
> morten
>
>
>
>
> Morten Mattingsdal wrote:
>   
>> Hello everyone,
>>
>> Ive managed to get the oligo package and the crlmm function up and 
>> running. Ive also installed the meta-data libraries from this URL 
>> http://www.biostat.jhsph.edu/~bcarvalh/oligoAddOns.tar.gz
>> provided by Benliton
>>
>> but when I run the commands:
>>
>>  >files <- list.celfiles()
>>  >snpFSet <- read.celfiles(files)
>>  >
>>  >Welcome to the pd.Mapping250K_Nsp prototype pdInfo package
>>  >WARNING: DO NOT USE THIS PACKAGE FOR ANY ANALYSIS.
>>  >THIS PACKAGE IS FOR INTERFACE PROTOTYPE USE ONLY!
>>  >THE DATA HAS NOT BEEN VALIDATED AND LIKELY HAS ERRORS.
>>  >Have fun!
>>
>> Im am happy that this information is warning me, but to my point:
>> - When will the "safe" mapping libraries come?
>> - Can I build this by myself ?
>>
>> I want to compare brlmm from Affymetrix and crlmm from BioC genotype 
>> calls for my data
>>
>> regards
>> morten
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>> .
>>
>>
>>     
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 07 Mar 2007 08:49:07 -0500
> From: "James W. MacDonald" <jmacdon at med.umich.edu>
> Subject: Re: [BioC] crlmm warning
> To: Morten Mattingsdal <mortenm at inbox.com>
> Cc: BioC <bioconductor at stat.math.ethz.ch>
> Message-ID: <45EEC2D3.6000504 at med.umich.edu>
> Content-Type: text/plain;  charset="utf-8";  format=flowed
>
> Morten Mattingsdal wrote:
>
>   
>> I find it ... non-trivial.. to locate the fasta file for Nsp and Sty 
>> arrays, but I think Ill harass Affyemtrix Inc for that.
>>
>>     
>
> These files are available on the support page for the 500K snp arrays 
> (near the bottom).
>
> http://www.affymetrix.com/support/technical/byproduct.affx?product=500k
>
>