Hi everyone, While I am running these command lines: library(oligo) celFiles <- list.celfiles() celFiles <- list.celfiles("expressionData", full.names=TRUE) Data <- read.celfiles(celFiles) I got this error: All the CEL files must be of the same type. Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE All CEL files are hg-1.1-st-Array. May someone let me know how I could solve this problem. Thanks, Jerry [[alternative HTML version deleted]]

Hi Jerry, On Thursday, November 07, 2013 12:18:27 PM, Jerry Cholo wrote: > > > Hi everyone, > > > > While I am running these command lines: > > library(oligo) > > > > celFiles <- list.celfiles() What do you get from typing celFiles at an R prompt right after this? > > celFiles <- list.celfiles("expressionData", full.names=TRUE) What is 'expressionData'? A subdirectory of your working directory? Again, what do you get when you type celFiles at an R prompt? > > Data <- read.celfiles(celFiles) > > > > I got this error: > > > > All the CEL files must be of the same type. > > Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE Note that you will get this error in two situations: 1.) The celFiles vector contains the names of different array types 2.) The celFiles vector is empty. > celFiles <- list.celfiles("somerandomthing", full.names = TRUE) > celFiles character(0) > read.celfiles(celFiles) All the CEL files must be of the same type. Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE > > > > All CEL files are hg-1.1-st-Array. May someone let me know how I could > solve this problem. The BEST way to solve this problem is to figure out for yourself what is happening. I realize this list is nice, and you can get answers quickly. However, you should think of the help you get here as being a limited resource. If it appears you are using more than your fair share, then you will find your questions going unanswered. Best, Jim > > > > Thanks, > Jerry > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099