Question: TAG3 script
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gravatar for Joshi, Nina NIH/NCI
14.8 years ago by
Joshi, Nina NIH/NCI40 wrote:
I am trying to create an affybatch from the cel files for the TAG3 chips (custom DNA arrays made by affy of the diploid and yeast haploid deletion strain) using the ReadTAG3 array script (written by Rafeal) on UNIX using R version 1.8.1, but I am receiving the following error: ? ? Error in eval.with.vis(expr, envir, enclose): Object "KIND." not found ? I would appreciate any information about this error or any suggestions, advice or comments on retrieving creating an affybatch using the cel files. ? Note: the script is attached Thanks, ? Nina ? ? -------------- next part -------------- ##THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND. ReadTAG3 <- function(filename="Tag3_ID.txt", CDFfile = "TAG_3.CDF", CELfiles = NULL, compress.cel = FALSE, compress.cdf = FALSE, verbose = T, chip.names = NULL, rm.mask = FALSE, rm.outliers = FALSE, rm.extra = FALSE, cdf.name = NULL, ...) { ##FIRST CHOOSE FILES ##with widget ##or without files <- list.files(...) if (is.null(CDFfile)) CDFfile <- files[grep(".[cC][dD][fF]", files)] if (length(CDFfile) != 1) stop(paste("CDFfile is not specified,exactly one CDF file must exist in path.\n")) if (is.null(CELfiles)) CELfiles <- files[grep(".[cC][eE][lL]", files)] nchips <- length(CELfiles) if (nchips < 1) stop(paste("CELfiles is not specified, at least one CEL file must exist in path.\n")) if (is.null(chip.names)) { chip.names <- CELfiles chip.names <- as.character(sapply(chip.names, function(x) strsplit(x,"\\.")[[1]][1])) } else { if (length(chip.names) != nchips) { warning("Not the same number of chips than chip names. Assigning names from file.\n") chip.names <- CELfiles chip.names <- as.character(sapply(chip.names, function(x) strsplit(x,"\\.")[[1]][1])) } } if (verbose) cat("reading CDF file\n") cdf <- read.cdffile(CDFfile, compress = compress.cdf) if (verbose) cat("processing information\n") info <- read.table(filename,header=T,sep="\t",as.is=T) upordown <- info[,"Plate"] upordown <- sapply(upordown,function(x) if(length(grep("U",x)>0)) return("U") else return("D")) geneNames <- info[,"Name"] tagNames <- info[,"Tag.name"] names(geneNames) <- tagNames names(upordown) <- tagNames probeNames <- cdf@name.levels[as.vector(cdf@name)] nrow <- dim(cdf@name)[1] ncol <- dim(cdf@name)[2] xs <- rep(0:(nrow-1), ncol) ys <- rep(0:(ncol-1), rep(nrow, ncol)) Index <- probeNames%in%tagNames mmindex <- which(ys%%4==2 & Index) pmindex <- which(ys%%4==1 & Index) cpmindex <- pmindex+2*nrow cmmindex <- mmindex+2*nrow probeNames <- probeNames[pmindex] nprob <- length(pmindex) x <- xs[pmindex] y <- ys[pmindex] pm <- matrix(0, nprob, nchips) mm <- matrix(0, nprob, nchips) cpm <- matrix(0,nprob, nchips) cmm <- matrix(0,nprob, nchips) if (verbose) cat("reading", nchips, "CEL files") for (i in 1:nchips) { aux <- as.vector(read.affybatch(filenames=CELfiles[i])@exprs) if (nrow * ncol != length(aux)) stop(paste(CELfiles[i], "doesn't match with CDFfile\n")) pm[, i] <- aux[pmindex] mm[, i] <- aux[mmindex] cpm[, i] <- aux[cpmindex] cmm[, i] <- aux[cmmindex] if (verbose) cat(".") } if (verbose) cat("\npreparing probe level object\n") ## generate probenames for each probe using cdf@name.levels and probe.ids probe.ids <- as.vector(cdf@name)[pmindex] probe.names <- cdf@name.levels[probe.ids] colnames(pm) <- chip.names rownames(pm) <- probeNames colnames(mm) <- chip.names rownames(mm) <- probeNames colnames(cpm) <- chip.names rownames(cpm) <- probeNames colnames(cmm) <- chip.names rownames(cmm) <- probeNames list(pm=pm,mm=mm,cpm=cpm,cmm=cmm,geneNames=geneNames[probeNames], probeNames=probeNames,upordown=upordown[probeNames],x=x,y=y) }
yeast cdf probe affy • 477 views
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