Hello list, In our lab we are trying to implement the GOstat package in microarray data analysis of UHN 12K chips. This is the model of our output file after analysis "Row" "Col" "ProbeUID" "ControlType" "ProbeName" "GeneName" "SystematicName" "logFC" "AveExpr" "t" "P.Value" "adj.P.Val" "B" "4489" 79 25 4792 0 "UHNhscpg0007521" "CASP9" NA 2.35039516877896 6.66036864568585 6.34745569917956 0.00285473198138345 0.996108545606581 -4.49478792330771 "5004" 79 60 5339 0 "UHNhscpg0007485" "KLK2" NA 2.59112634052802 6.86770306089859 6.27908218635525 0.00297451703773736 0.996108545606581 -4.49505386268111 I have tried differant parameters from the output file for proper analysis in GOstat but none of them worked, it will be very helpfull if anyone can suggest me the appropriate input parameters for the package , taking into consideration the above model of data. A.Ashwin Department of Biotechnology Manipal Life Science Center Manipal University INDIA [[alternative HTML version deleted]]

Hi Ashwin, Ashwin Kumar wrote: > Hello list, > > In our lab we are trying to implement the GOstat package in microarray data > analysis of UHN 12K chips. What exactly is a UHN 12K chip? > This is the model of our output file after analysis > > "Row" "Col" "ProbeUID" "ControlType" "ProbeName" > "GeneName" "SystematicName" "logFC" "AveExpr" "t" > "P.Value" "adj.P.Val" "B" > "4489" 79 25 4792 0 "UHNhscpg0007521" "CASP9" NA > 2.35039516877896 6.66036864568585 6.34745569917956 > 0.00285473198138345 0.996108545606581 -4.49478792330771 > "5004" 79 60 5339 0 "UHNhscpg0007485" "KLK2" NA > 2.59112634052802 6.86770306089859 6.27908218635525 > 0.00297451703773736 0.996108545606581 -4.49505386268111 > > I have tried differant parameters from the output file for proper analysis > in GOstat but none of them worked, it will be very helpfull if anyone can > suggest me the appropriate input parameters for the package , taking into > consideration the above model of data. The appropriate input would be Entrez Gene IDs, but I don't see them here. I assume the manufacturer of this chip has some annotation file that includes some sort of reliable systematic ID? You can use the org.Hs.eg.db package (assuming these are human chips) to map to Entrez Gene and then can go from there. Best, Jim > > A.Ashwin > Department of Biotechnology > Manipal Life Science Center > Manipal University > INDIA > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826