[BioC] an error in AnnotationForge

[Marc Carlson]

On 08/04/2013 03:34 AM, joseph wrote:
> Dear Marc Carlson,
>
>   
>
> I'm using AnnotationForge to make my customized package, however, in
> affymetrix annotation file, some probes correspond to genes have more gene
> symbols, like this, "11715100_at" to "HIST1H3A /// HIST1H3B /// HIST1H3C ///
> HIST1H3D /// HIST1H3E /// HIST1H3F /// HIST1H3G /// HIST1H3H /// HIST1H3I
> /// HIST1H3J".
>
> So that, when I make package:
>
> makeDBPackage("HUMANCHIP_DB",
>
>                affy = TRUE,
>
>                prefix = "primeview",
>
>                fileName = "E:/Microarray Data/Affy array
> database/PrimeView.na33.annot.csv",
>
>                baseMapType = "ug",
>
>                version = "1.0.0",
>
>                manufacturer = "Joseph",
>
>                chipName = "primeview")
>
> Even it works, but this probes could not be matched to expression data, when
> I annotate it, the output looks like :
>
>                   Gene Symbol
>
> 11715100_at      11715100_at
>
> 11715104_s_at    OTOP2
>
> 11715105_at      C17orf78
>
>   
>
> Please tell me how to fix it out. Thanks!
>
>   
>
> Joe
>
>   

Hi Joe,

This doesn't look right, but you have given me no way to reproduce 
this.  Can you please send me your sessionInfo() and your input file?


Thanks,


   Marc


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