Hi everyone, I am trying to use Gene ST arrays data from this GSE number GSE48191. It has .CEL files. I used the following command library(oligo) celFiles <- list.celfiles("/home/user/Desktop/GSE48191_Iwasaki_affy/") celFiles [1] "GSM1171898_WT1_MoGene-1_0-st-v1_.CEL" "GSM1171899_WT2_MoGene-1_0-st-v1_.CEL" [3] "GSM1171900_WT3_MoGene-1_0-st-v1_.CEL" "GSM1171901_WT4_MoGene-1_0-st-v1_.CEL" [5] "GSM1171902_WT5_MoGene-1_0-st-v1_.CEL" "GSM1171903_KO1_MoGene-1_0-st-v1_.CEL" [7] "GSM1171904_KO2_MoGene-1_0-st-v1_.CEL" "GSM1171905_KO3_MoGene-1_0-st-v1_.CEL" [9] "GSM1171906_KO4_MoGene-1_0-st-v1_.CEL" "GSM1171907_KO5_MoGene-1_0-st-v1_.CEL" affyRaw <- read.celfiles(celFiles) I get this error Error: These do not exist: GSM1171898_WT1_MoGene-1_0-st-v1_.CEL GSM1171899_WT2_MoGene-1_0-st-v1_.CEL GSM1171900_WT3_MoGene-1_0-st-v1_.CEL GSM1171901_WT4_MoGene-1_0-st-v1_.CEL GSM1171902_WT5_MoGene-1_0-st-v1_.CEL GSM1171903_KO1_MoGene-1_0-st-v1_.CEL GSM1171904_KO2_MoGene-1_0-st-v1_.CEL GSM1171905_KO3_MoGene-1_0-st-v1_.CEL GSM1171906_KO4_MoGene-1_0-st-v1_.CEL GSM1171907_KO5_MoGene-1_0-st-v1_.CEL Also since they used Affymetrix Mouse Gene 1.0 ST Array I should use this package pd.mogene.1.0.st.v1 Any help how can i remove the error and then how can I add Gene Annotation to Normalized Expression Output?? Regards Varun [[alternative HTML version deleted]]

Hi Varun, On 7/22/2014 3:11 PM, VG wrote: > Hi everyone, > I am trying to use Gene ST arrays data from this GSE number GSE48191. > It has .CEL files. > I used the following command > > library(oligo) > celFiles <- list.celfiles("/home/user/Desktop/GSE48191_Iwasaki_affy/") This only works if you are reading celfiles from your working directory. From ?list.celfiles: Note: Quite often users want to use this function to pass filenames to other methods. In this situations, it is safer to use the argument 'full.names=TRUE'. In other words, list.celfiles() by itself will just list all the celfiles in a given directory. If you also want to point to that directory, you need to include full.names = TRUE. Alternatively, you can do setwd("/home/user/Desktop/GSE48191_Iwasaki_affy/") affyRaw <- read.celfiles(list.celfiles()) Best, Jim > > celFiles > [1] "GSM1171898_WT1_MoGene-1_0-st-v1_.CEL" > "GSM1171899_WT2_MoGene-1_0-st-v1_.CEL" > [3] "GSM1171900_WT3_MoGene-1_0-st-v1_.CEL" > "GSM1171901_WT4_MoGene-1_0-st-v1_.CEL" > [5] "GSM1171902_WT5_MoGene-1_0-st-v1_.CEL" > "GSM1171903_KO1_MoGene-1_0-st-v1_.CEL" > [7] "GSM1171904_KO2_MoGene-1_0-st-v1_.CEL" > "GSM1171905_KO3_MoGene-1_0-st-v1_.CEL" > [9] "GSM1171906_KO4_MoGene-1_0-st-v1_.CEL" > "GSM1171907_KO5_MoGene-1_0-st-v1_.CEL" > > affyRaw <- read.celfiles(celFiles) > > I get this error > Error: These do not exist: > GSM1171898_WT1_MoGene-1_0-st-v1_.CEL > GSM1171899_WT2_MoGene-1_0-st-v1_.CEL > GSM1171900_WT3_MoGene-1_0-st-v1_.CEL > GSM1171901_WT4_MoGene-1_0-st-v1_.CEL > GSM1171902_WT5_MoGene-1_0-st-v1_.CEL > GSM1171903_KO1_MoGene-1_0-st-v1_.CEL > GSM1171904_KO2_MoGene-1_0-st-v1_.CEL > GSM1171905_KO3_MoGene-1_0-st-v1_.CEL > GSM1171906_KO4_MoGene-1_0-st-v1_.CEL > GSM1171907_KO5_MoGene-1_0-st-v1_.CEL > > Also since they used Affymetrix Mouse Gene 1.0 ST Array I should use this > package > pd.mogene.1.0.st.v1 > > Any help how can i remove the error and then how can I add Gene Annotation > to Normalized Expression Output?? > > Regards > Varun > > [[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