[BioC] ragene10st

[Marc Carlson]

Hi Sebastien,

The affy parameter is just a shortcut for affymetrix expression arrays. 
If you want to use that parameter, then you can download the appropriate
annotation library file from Affymetrix website (which you probably have
to get anyhow), just point to it in the parameter and then call the
function.  What SQLforge will then try to do is to parse this file by
removing from it only the probeset IDs and the entrez gene, refseq IDs
and unigene IDs from the file in order to sort out what all these genes
are and thus generate the files that are described in the vignette from
this affymetrix file.  This will work as long as this particular
annotation file is formatted similarly to what has come before.   But,
really this parameter is purely for convenience and not at all necessary
to using SQLForge.  A lot of people use affy, so I just added this to
make it easier for that majority of users. 

You almost as easily  can just grab that same Affymetrix annotation
library file and make the tab delimited files that I described
yourself.  All you really need is a file that tells the gene identity of
the different probesets.  So you can ignore the vast majority of the
data in the file.  If you have that, then you have all that you really
need to proceed.  For most platforms this just means selecting out tow
of the columns and then creating a tab file from those.  Then you have
to feed such a file to your function.

Please let me know if you have more questions,


  Marc





Sebastien Gerega wrote:
> Hi Marc and thanks for your help. I've had a look at the SQLForge
> vignette and there are still a couple issues that are unclear to me.
> Firstly, for the Rat Gene ST arrays is it possible to use any of the
> annotation files from the Affymetrix site as input for makeRATCHIP_DB
> in AnnotationDbi? If not, and the list of probes has to be manually
> created what is the best way to go about doing this?
> thanks again,
> Sebastien
>
>
> Marc Carlson wrote:
>> Hi Sebastien,
>>
>> We have just never had anyone ask for one before.  However, you can make
>> a package for yourself if you follow the instructions in the SQLForge
>> vignette in the AnnotationDbi package:
>>
>> http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi.html
>>
>> Please let me know if you have further questions regarding this.
>>
>>   Marc
>>
>>
>> Sebastien Gerega wrote:
>>  
>>> Hi,
>>> I have been analysing human and mouse gene ST chips using a
>>> combination of the Aroma package and the hugene10st.db and
>>> mogene10st.db annotation packages. Now I am attempting to perform the
>>> same on some rat gene ST chips but have unable to find the
>>> corresponding annotations. Why is there no ragene10st?
>>> thanks,
>>> Sebastien
>>>
>>> _______________________________________________
>>> 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
>>>
>>>     
>>
>>
>>   
>
>