On Wed, May 12, 2010 at 2:43 AM, varpal singh <gilvarpal@gmail.com> wrote:

> Thanks for your reply !!    I have a list of arrays like 259879_at,
> 250464_at, 253416_at,
> 257506_at, 259790_s_at. These are the 5 arrays of my 198 arrays.
> I think you are talking about these array, if you are talking abt other ,
> please let me know, I would like to tell the name of experiment GSE2133,
> first I compared AIR Vs ANOXIA CEL files.
>
>
Please, Varpal, use "Reply to All" when answering email from the list.

If you are using GSE2133, that is run on GPL 198, which is called
"[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array".  That is the name
of the chip.  Go to the bioconductor website and look at the metadata
packages available:

http://bioconductor.org/packages/2.6/data/annotation/

Find the appropriate annotation package for your array.  There is an
annotation package that appears to match your chip type:

http://bioconductor.org/packages/2.6/data/annotation/html/ath1121501.db.html

Install this package using biocLite().

Then, read the vignette from the AnnotationDbi package that is entitled
"AnnotationDbi: How to use the ".db" annotation packages".  After reading
that, it should be relatively clear how you can accomplish your task given
that you are starting with Affy IDs.


> I want to get their entrez ids only.
>
> I have also found a code for entrez ids like
> x<-org.At.tairENTREZID
> #get the ORF IDs that are mepped to an ENTREZ gene ID#
> meped_gene<-mappedkeys(x)
> #convert to a list
> xx<-as.list(x[meped_gene])
> if(length(xx)>0) {
> #get the entrez gene ids for the first five genes
> xx[1:5]}
>
> But I want just 198 entrez ids of genes. In this code I could not
> understand how can I introduc
> my genes 198 that is problem here..
>
> Can you tell me if you have an idea ??
>
>
Follow the AnnotationDbi vignette with the appropriate annotation package
(given above).  If you have questions after going through the AnnotationDbi
vignette, be sure to provide the code you are using as a reproducible
example, any error messages, and the output of sessionInfo() when asking
where to go next.

Sean



> Varpall
>
>
> On Wed, May 12, 2010 at 1:15 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:
>
>>
>>
>> On Tue, May 11, 2010 at 10:18 AM, varpal singh <gilvarpal@gmail.com>wrote:
>>
>>> Dear Madam/SIr,
>>>
>>> I would like to know how can I get entrez id for arabidopsis, on the
>>> basis
>>> of probe ids in microarray by  bioconductor ??
>>> I have 198 genes after cut-off for P .value 0.05 and logFC value less
>>> than
>>> -2 and greater than 2....
>>> I used affymetrix data,
>>>
>>>
>> What is the name of the array?  That is the important piece that is
>> missing here.
>>
>> Sean
>>
>>
>>>  I got a reply from bioconductor lists in which they suggested me for
>>> *org.At.tair.db
>>> *and also send me script but that is not working, like
>>>
>>> > library(ag.db)
>>> > id<-c("259879_at")
>>> >  accs=toTable(agACCNUM[id])
>>> Error in .checkKeys(value, Lkeys(x), x@ifnotfound) :
>>>  value for "259879_at" not found
>>> Error in toTable(agACCNUM[id]) :
>>>  error in evaluating the argument 'x' in selecting a method for function
>>> 'toTable'
>>>
>>> am not getting my result, please let me know how can I get entrez ids for
>>> my
>>> 198 genes in arabidopsis..
>>>
>>> Thanks &&Regards
>>> Varpal
>>>
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>>>
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>>
>>
>

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