Question: an error in AnnotationForge
0
gravatar for joseph
6.4 years ago by
joseph40
joseph40 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 [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.4 years ago by Marc Carlson7.2k • written 6.4 years ago by joseph40
Answer: an error in AnnotationForge
0
gravatar for Marc Carlson
6.4 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
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 > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 6.4 years ago by Marc Carlson7.2k
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