[BioC] Query regarding entrez id

[Marc Carlson]

Hi Varpal,

Could you please post the results of calling sessionInfo() ?  The
problem you are having with the example I gave you is almost certainly
caused by the probe IDs not being mapped to a TAIR ID in some older
annotations.  So you could probably just do this 1st to make it work:

library(ag.db)
ids = c("11987_at","11988_at","11989_at")
##add this one extra line
cleanIds = ids[ids %in% mappedLkeys(agACCNUM)]
probeTAIR = toTable(agACCNUM[ids])
merge(probeTAIR, toTable(org.At.tairENTREZID))


  Marc

 

On 05/11/2010 07:18 AM, varpal singh 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,
>
> 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 at 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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