Hi, I am currently trying to annotate affy data and export it to a HTML file. I'm having problems with the following codes: library(multtest) class <- as.integer(pData(Gds2609)$covar1) ? 1 teststat <- mt.teststat(exprs(Gds2609), class) index <- order(abs(teststat), decreasing = TRUE) probeids <- featureNames(Gds2609)[index] I get error warning messages when I do class and when I try to do teststat R stops working. Any help that anyone could give me would be gratefully received. Best Wishes, Katie

On Mon, May 17, 2010 at 9:03 AM, Katie <kt70@le.ac.uk> wrote: > Hi, > > I am currently trying to annotate affy data and export it to a HTML file. > I'm > having problems with the following codes: > > library(multtest) > class <- as.integer(pData(Gds2609)$covar1) – 1 > teststat <- mt.teststat(exprs(Gds2609), class) > index <- order(abs(teststat), decreasing = TRUE) > probeids <- featureNames(Gds2609)[index] > > I get error warning messages when I do class and when I try to do teststat > R > stops working. Any help that anyone could give me would be gratefully > received. > > Hi, Katie. Since you did not provide the error message or the output of sessionInfo(), it is hard to know what the problem is, but I suspect it might have to do with the fact that "class" is a function in R and reassigning it to be an integer vector might break things. Try removing the "class" variable and use another variable name. If that isn't the issue, be sure to read the posting guide before writing back. Sean [[alternative HTML version deleted]]