[BioC] Starr package: cmarrt.ma error

[Umassmed]

Paul,

I downloaded Bpmap file from cisGenome website,that solved the issue.

Best regards,

Julie

> On Apr 3, 2014, at 5:23 PM, Paul <paul.guilhamon.10 at ucl.ac.uk> wrote:
> 
> Zhu, Lihua (Julie <Julie.Zhu at ...> writes:
> 
>> 
>> Benedikt,
>> 
>> I encountered the following error using Starr package to analyze chip-chip
> data from GeneChip Human
>> Promoter 1.0R Array 
>> http://www.affymetrix.com/estore/esearch/search.jsp?
> pd=131461&N=4294967292. Could you please help?
>> 
>> In addition, there are two bpmap files: Hs_PromPF_v02-3_NCBIv34.bpmap and
>> Hs_PromPR_v02-3_NCBIv34.bpmap for this array. Is there a way to pass both
> bpmap files to readBpmap function?
>> 
>> Many thanks for your help in advance!
>> 
>> Best regards,
>> 
>> Julie
>> 
>>> h3k27R_loess_ratio <- getRatio(h3k27R_loess, ips, controls, description,
> fkt=median, featureData=F)
>> Calculating ratio
>> Building new ExpressionSet
>> 
>>> peaks <- cmarrt.ma(h3k27R_loess_ratio, probeAnnoR, chr=NULL, M=NULL,
> frag.length=146)
>> Error in probeAnno[paste(x, "start", sep = ".")] :
>>  No mapping 'Bs:Jan_2004;NC_000964.start' in this 'probeAnno' object.
> 
> 
> Hi Julie,
> Just wondering if you got an answer to your question or figured it out 
> somehow? I'm getting the exact same error (I'm analyzing medip-chip data)
> No mapping 'Bs: Jan_2004;NC_000964.start' in this 'probeAnno' object.
> 
> Thanks!
> 
> Paul
> 
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