[BioC] ragene10st

[Groot, Philip de]

Hello Marc,
 
Yes, I agree! But I do see a problem though. The hugene10st and mogene10st annotation packages are build utilizing multiple sources, not only genbank or entrezg. That's what makes this package different compared to the other 2 and the reason that I feel that this package is not "compliant". Correct me if I am wrong.
 
Additionally. I do not understand why the ragene10st arrays are not simply made available by the core team? Human and mouse is. Only rat is lacking (more ST arrays are not available at the moment).
 
Regards,
 
Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail:   Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl> 
Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/> 
             http://humannutrition.wur.nl <http://humannutrition.wur.nl/> 
             https://madmax.bioinformatics.nl <https://madmax.bioinformatics.nl/> 
 
 
 

________________________________

Van: Marc Carlson [mailto:mcarlson at fhcrc.org]
Verzonden: ma 09/03/2009 04:52
Aan: Groot, Philip de
CC: bioconductor at stat.math.ethz.ch
Onderwerp: Re: [BioC] ragene10st



Hi Philip,

The ACCNUM does not refer to the Affymetrix probe IDs, but rather to the
genbank IDs, which were not included in the construction of this
particular package (hence their absence).  For most people, this is not
going to be much of a problem (and is unlikely to be a problem at all).
The fact that this is a chip package means that for the vast majority of
the mappings present, the Lkeys(mapName) will be Affymetrix probes
otherwise, those mappings would not have any mapped keys.

Hope this clarifies things,


  Marc




Groot, Philip de wrote:
> Hello Sebastien,
> 
> I checked out your ragene10st.db library and found the following:
> 
>  
>> ragene10st()
>>    
> Quality control information for ragene10st:
>
> This package has the following mappings:
> ragene10stACCNUM has 0 mapped keys (of 29216 keys)
> ragene10stALIAS2PROBE has 30979 mapped keys (of 30979 keys)
> ragene10stCHR has 19932 mapped keys (of 29216 keys)
> ragene10stCHRLENGTHS has 23 mapped keys (of 23 keys)
> ragene10stCHRLOC has 14225 mapped keys (of 29216 keys)
> ragene10stCHRLOCEND has 14225 mapped keys (of 29216 keys)
> ragene10stENSEMBL has 18339 mapped keys (of 29216 keys)
> ragene10stENSEMBL2PROBE has 17366 mapped keys (of 17366 keys)
> ragene10stENTREZID has 29216 mapped keys (of 29216 keys)
> ragene10stENZYME has 1494 mapped keys (of 29216 keys)
> ragene10stENZYME2PROBE has 692 mapped keys (of 692 keys)
> ragene10stGENENAME has 19953 mapped keys (of 29216 keys)
> ragene10stGO has 14583 mapped keys (of 29216 keys)
> ragene10stGO2ALLPROBES has 9863 mapped keys (of 9863 keys)
> ragene10stGO2PROBE has 7437 mapped keys (of 7437 keys)
> ragene10stMAP has 19502 mapped keys (of 29216 keys)
> ragene10stPATH has 4201 mapped keys (of 29216 keys)
> ragene10stPATH2PROBE has 206 mapped keys (of 206 keys)
> ragene10stPFAM has 19087 mapped keys (of 29216 keys)
> ragene10stPMID has 12157 mapped keys (of 29216 keys)
> ragene10stPMID2PROBE has 34899 mapped keys (of 34899 keys)
> ragene10stPROSITE has 19087 mapped keys (of 29216 keys)
> ragene10stREFSEQ has 19869 mapped keys (of 29216 keys)
> ragene10stSYMBOL has 19953 mapped keys (of 29216 keys)
> ragene10stUNIGENE has 18427 mapped keys (of 29216 keys)
> ragene10stUNIPROT has 10050 mapped keys (of 29216 keys)
>
> Additional Information about this package:
> DB schema: RATCHIP_DB
> DB schema version: 1.0
> Organism: Rattus norvegicus
> Date for NCBI data: 2008-Sep2
> Date for GO data: 200808
> Date for KEGG data: 2008-Sep2
> Date for Golden Path data: 2006-Jun20
> Date for IPI data: 2008-Sep02
> Date for Ensembl data: 2008-Jul23
>
> That ACCNUM has 0 entries is weird. EntrezID entries are all found... So, you build this package on EntrezIDs and not on the AFFYIDs that are usually provided. So your library won't work properly for people whom simply download it blindly! Just to let you know. Perhaps you should consider to take it offline and to only provide it if people ask for it AND realise the problems with it?
> 
> Regards,
> 
> Dr. Philip de Groot Ph.D.
> Bioinformatics Researcher
>
> Wageningen University / TIFN
> Nutrigenomics Consortium
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> PO Box 8129, 6700 EV Wageningen
> Visiting Address: Erfelijkheidsleer: De Valk, Building 304
> Dreijenweg 2, 6703 HA  Wageningen
> Room: 0052a
> T: +31-317-485786
> F: +31-317-483342
> E-mail:   Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl>
> Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/>  <http://www.nutrigenomicsconsortium.nl/>
>              http://humannutrition.wur.nl <http://humannutrition.wur.nl/>  <http://humannutrition.wur.nl/>
>              https://madmax.bioinformatics.nl <https://madmax.bioinformatics.nl/>  <https://madmax.bioinformatics.nl/>
> 
> 
> 
>
> _______________________________________________
> 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
>
>