Question: 答复: an error in AnnotationForge
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gravatar for joseph
6.3 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 6.3 years ago • written 6.3 years ago by joseph40
Answer: 答复: an error in AnnotationForge
0
gravatar for joseph
6.3 years ago by
joseph40
joseph40 wrote:
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]]
ADD COMMENTlink written 6.3 years ago by joseph40
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