search for: readtarget

...[1:22690, 1:2] 12.0 11.3 13.0 11.6 10.3 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:22690] "1415670_at" "1415671_at" "1415672_at" "1415673_at" ... ..$ : chr [1:2] "A1_xen1_1_1.CEL" "A2_xen2a_5_2.CEL" targets<-readTargets("xen1shrt.txt") # Read target files >targets Name FileName Target 1 A1_xen1_1_1 A1_xen1_1_1.CEL A_xen 2 A2_xen2a_5_2 A2_xen2a_5_2.CEL A_xen 3 A3_xen2b_6_3 A3_xen2b_6_3.CEL A_xen 4 B1_cr1_2_4 B1_cr1_2_4.CEL B_crp 5 B2_cr2a_9_5 B2_cr2a_9_5.CEL B_crp 6 B...

...per array or the mean of all the controls per array. The gal file is also loaded with all the array structure. Each block contains spike in controls. Here is the code: library(limma) library(RColorBrewer) library(vsn) Cy5 <- "F635 Mean" 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 c...

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...f 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 TS <- paste(targets$Species, targets$Time, sep=".") #This script returns the following: TS # Turn TS into a factor variable which facilitates fitting TS <- factor(TS) #This script retu...

...ing. Will the above-mentioned warnings affect the reliability of the final result? Can I continue to the next step? Thanks! Dejian Zhao ++++++++++++++++++ Program Starts +++++++++++++++++++++ > library(limma) > library(statmod) #duplicateCorrelation requires this package. > targets<-readTargets() > targets Cy3 Cy5 FileName Date 1 PLAIN PLATEAU Locust 186.gpr 2006-5-31 2 PLAIN PLATEAU Locust 187.gpr 2006-5-31 3 PLAIN PLATEAU Locust 188.gpr 2006-5-31 4 PLAIN PLATEAU Locust 189.gpr 2006-5-31 5 PLAIN PLATEAU Locust 190.gpr 2006-5-31 6 PLAIN PLATEAU...