[BioC] ragene10st

[Marc Carlson]

Well one way is to navigate Affymetrix's website and grab the annotation
file

http://www.affymetrix.com/support/technical/annotationfilesmain.affx

Or you could also use Martin Morgans clever AffyCompatible package which
will let you get the data you need more directly.

##The 2nd approach would go something like this (adapting from Martins
Vignette):
library(AffyCompatible)
password <- "your_psswd"
rsrc <- NetAffxResource(user="you at someplace.com", password=password)
head(names(rsrc))
affxDescription(rsrc[["RaGene-1_0-st-v1"]])
annos <- rsrc[["RaGene-1_0-st-v1"]]
annos
sapply(affxAnnotation(annos), force)
anno <- rsrc[["RaGene-1_0-st-v1", "Probeset Annotations, CSV Format"]]
fl <- readAnnotation(rsrc, annotation=anno, content=FALSE)
fl
conn <- unz(fl, "RaGene-1_0-st-v1.na27.2.rn4.probeset.csv")
##Then get a dataframe with the contents of the file in it
df = read.table(conn, header=TRUE, skip=18, sep=",")



  Marc




Sebastien Gerega wrote:
> 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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>>>>> Search the archives:
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>>>>>
>>>>>             
>>>>         
>>>     
>>
>>
>>   
>
>