an error in AnnotationForge
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joseph ▴ 40
@joseph-5658
Last seen 4.5 years ago
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]]
Annotation ChipName annotate affy AnnotationForge Annotation ChipName annotate affy • 704 views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.8 years ago
United States
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
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