[BioC] ragene10st

[Sebastien Gerega]

Hi Marc,
I guess the problem lies in the fact that I don't know which Annotation 
file to use. I can't seem to find any that have the appropriate columns. 
What files were used to generate mogene10st.db and hugene10st.db ? I can 
find appropriate annotations for Affy 3' arrays but not for the Gene St 
ones....
thanks again,
Sebastien


Marc Carlson wrote:
> 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
>>>>
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>>>>
>>>>     
>>>>         
>>>   
>>>       
>>     
>
>
>