Hello group, Iam a novice in microarray data analysis. I am using R version 2 and Bioconductor version 1.5. My experiment is to read some cel files from a directory and to derive expression values. > library(Biobase) > library(affy) >library(hgu133a) > data <- read.affybatch("lung.CEL","HEART.CEL","PROSTATE.CEL","UTERUS .CEL","LIVER.CEL") Warning message: Incompatible phenoData object. Created a new one. in: read.affybatch("3AJW02021805_lung.CEL", "3AJZ02021909_HEART.CEL", > dim(data) NULL I do not understand this problem. I have seen my friend using R version 1.9 has no problem with same files. Is this a bug in R 2.0 or am i committing a mistake here. Could any one help me , please. Thank you. Salil

Hi Salil, This is just a simple misunderstanding. What you have to understand is that you are instantiating an AffyBatch object that has different 'slots' that can contain different information (type class ?AffyBatch at an R prompt for more information). There is a slot (the pData slot) that can contain a data.frame() that lists out the phenotypic data for your different samples. Since you didn't specify anything, read.affybatch() made something up for you. If you type pData(data), you will see what is in that particular slot. Note here that 'data' is a bad variable name because you are masking an existing R function called data(). I prefer to use e.g., dat, or Data. Since the AffyBatch is an object with several slots, dim(data) doesn't make any sense, so you get NULL returned. There are several accessor functions that can be used to look at the data contained in your AffyBatch. Again, see class ?AffyBatch for more information. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> SALIL SHARMA <ssharma@jhmi.edu> 03/25/05 5:08 PM >>> Hello group, Iam a novice in microarray data analysis. I am using R version 2 and Bioconductor version 1.5. My experiment is to read some cel files from a directory and to derive expression values. > library(Biobase) > library(affy) >library(hgu133a) > data <- read.affybatch("lung.CEL","HEART.CEL","PROSTATE.CEL","UTERUS.CEL","LIV ER.CEL") Warning message: Incompatible phenoData object. Created a new one. in: read.affybatch("3AJW02021805_lung.CEL", "3AJZ02021909_HEART.CEL", > dim(data) NULL I do not understand this problem. I have seen my friend using R version 1.9 has no problem with same files. Is this a bug in R 2.0 or am i committing a mistake here. Could any one help me , please. Thank you. Salil _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.