Hello everybody, haw can I retrieve easily from an RGlist object the row value of a specific gene if I know only the "Gene ID"? thank you all and forgive me to bother you with basic questions! Emanuele

Hello everybody, if I want to know the absolute level expression of a specific gene, how can I retrieve the value,the postion in the slide,etc only knowing the "Gene ID" of the RG$genes slot? to do that I perform a loop to calculate the index...but I'm sure there must be an easiest way! please somebody say something! sorry again if for you it's a stupid question regards. Em _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Hi Emanuele, > Hello everybody, > haw can I retrieve easily from an RGlist object the row value of a > specific gene if I know only the "Gene ID"? thank you all and forgive me > to bother you with basic questions! > > Emanuele If you have the R/G information stored in an RGList object (called RG), the gene names stored in RG$genes, and you known the ID, or name (say "AAX3"), then subsetting your RGList as follows should give you what you want. RG[RG$genes$ID=="AAX3",] See below for a working example. Best wishes, Matt Ritchie # Make up a dummy genelist gal <- as.data.frame(cbind(Block=rep(1,10), Column=seq(1:10), Row=rep(1,10), ID=c("Control 1", "Control 2", "AAX1", "AAX2", "AAX3", "AAX4", "AAX5", "AAX6", "AAX7", "AAX8"),Name=c("House keeping 1", "House keeping 2", "AAX1", "AAX2", "AAX3", "AAX4", "AAX5", "AAX6", "AAX7", "AAX8"))) gal # Make up an RGList object, for 2 arrays with 10 genes on each RG <- new("RGList", list(R=matrix(rnorm(20, 1000, 300), 10,2), G=matrix(rnorm(20, 1500, 350),10,2), Rb=NULL, Gb=NULL, genes=gal, printer=list(nspot.r=1, nspot.c=10, ngrid.r=1, ngrid.c=1))) RG # Show the RG information for the gene that you're interested in RG[RG$genes$ID=="AAX3",]