I am using limma package for identifying differential expression of affymetrix .CEL file. I used quantile normalization method and saved the normalized data in .txt file. However, i am not able to import the .txt file into limma for differential expression. Kindly tell me the sequential procedure for identifying the differential expression of quantile normalized data. -- output of sessionInfo(): aa -- Sent via the guest posting facility at bioconductor.org.

You will need to give more information than this if you want help. How are you pre-processing the data? Using R or something else? What have you tried, and what were the results? Note that you cannot import anything into limma - you import into R and then use limma to analyze the data. Also, have you read the limma User's Guide? If not, you should, as probably 99.325% (just an estimate) of your questions are covered in that document. http://www.bioconductor.org/packages/2.12/bioc/vignettes/limma/inst/do c/usersguide.pdf Best, Jim On Tuesday, September 24, 2013 9:04:07 AM, Dhanjit [guest] wrote: > > I am using limma package for identifying differential expression of affymetrix .CEL file. I used quantile normalization method and saved the normalized data in .txt file. However, i am not able to import the .txt file into limma for differential expression. > > Kindly tell me the sequential procedure for identifying the differential expression of quantile normalized data. > > -- output of sessionInfo(): > > aa > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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