答复: 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 • 755 views
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Entering edit mode
joseph ▴ 40
@joseph-5658
Last seen 4.5 years ago
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 ·¢¼þÈË: joseph [mailto:joseph.houjue@gmail.com] ·¢ËÍʱ¼ä: 2013Äê8ÔÂ4ÈÕ 18:35 ÊÕ¼þÈË: bioconductor@r-project.org Ö÷Ìâ: Re: [BioC] an error in AnnotationForge ÖØÒªÐÔ: ¸ß 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]]
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