search for: readgal

...mber=7200); hist(res$P.Value,breaks=50); The error message I get is : Read ndd1_1.txt Read ndd1_2.txt Read ndd1_3.txt Error in switch(method, loess = { : Layout argument not specified I then created a layout file and added in the following code, but I still got the same error message. RG$genes=readGAL(); gal=readGAL(); layout=getLayout(gal); Also, when I type RG , I get, > RG An object of class "RGList" $R [1] 3 $Rb [1] 6 $G [1] 10 $Gb [1] 14 $targets FileName ndd1_1 ndd1_1.txt ndd1_2 ndd1_2.txt ndd1_3 ndd1_3.txt $source [1] "arrayvision" $genes Block...

...an" Cy5b <- "B635 Mean" targets <- readTargets("targets.txt") #My gpr files do only contain 1 channel (Cy5) RG <- read.maimages( targets$FileName,source="genepix",columns=list(R=Cy5,G=Cy5, Rb=Cy5b, Gb=Cy5b)) RG$G <- NULL RG$Gb <- NULL RG$genes <- readGAL("array_human_mirs.gal") #Here are my spike in controls for normalization isSpikeIn <- grep("CTL", RG$genes$Name) #The vsn normalization works fine mat <- vsnMatrix(RG$R) However i would like to normaliza using my spikein controls by block or by using the mean of all con...

...phenotypicdata) all(rownames(myphenotypicdata)==colnames(myexprdata)) #[1] TRUE #Create annotated Data Frame adf<-new("AnnotatedDataFrame",data=phenotypicdata) #dim means: dimension of an object. dim(adf) #rowNames columnNames # 28 2 rownames(adf) #NULL #read in galfile readGAL("Galfile.gal") #Create eset object eSet<-new("ExpressionSet",exprs=myexprdata,phenoData=adf,annotation="Galfile.gal") #Read in targets file targets <- readTargets("targets.txt") targets # Set up character list defining your arrays, include replicates...

...r Read Locust 190.gpr Read Locust 191.gpr Read Locust 192.gpr Read Locust 193.gpr Read Locust 194.gpr Read Locust 195.gpr Read Locust 196.gpr Read Locust 197.gpr Read Locust 198.gpr Read Locust 199.gpr Read Locust 200.gpr Read Locust 201.gpr Read Locust 202.gpr Read Locust 203.gpr > RG$genes<-readGAL() > spottypes<-readSpotTypes() > spottypes SpotType ID Name Color 1 gene * * black 2 blank Blank * brown 3 buffer *sc * blue 4 rice Os026* * green 5 beta-actin Beta* * red 6 18S 18S* * yellow 7 GAPDH GAPDH*...