One more question, if I make this db successfully, when I annotate
expression data, there are still some probeID could be annotated with gene
symbol, still show ProbeID. However, these probes truly have gene symbol
names. How to fix it out? 

 

PS. Administrator guy, please approve  this mail, maybe we had met before, I
worked in SCHARP. 

 

Jue Hou,Ph.D.

Research Assistant

 

Center of Medical Physics and Technology

Hefei Institutes of Physical Science

Chinese Academy of Sciences

No.350 Shushanhu Road,Shushan District,Heifei,P.R. China 

Tel. +86551-65595385

Email:  <mailto:joseph.houjue@gmail.com> joseph.houjue@gmail.com;
<mailto:houjue00722@sina.com> houjue00722@sina.com

 

 

发件人: joseph [mailto:joseph.houjue@gmail.com] 
发送时间: 2013年8月4日 18:35
收件人: bioconductor@r-project.org
主题: Re: [BioC] an error in AnnotationForge
重要性: 高

 

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

 

 

 


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