Dear All, I normalised and summarised my data using gcrma() routine and have the expression values for each probeset. I now want to do the comparison between two classes of the samples (i.e. fold change between the classes). One thing I'm not sure is how to compare them because, as I read from the gcrma paper, the expression values after the gcrma() routine are log(intensity) after background adjustment. My question is: Do I have to convert the expression values from gcrma() back to raw values by e^(values) before calculate the fold change between the two classes that I have? Best Yot

take a look on chapter 11 of the limma user guide... there is one example with rma, which you will replace by gcrma on your example. b On 13 June 2011 14:46, yotsawat pomyen <yotsa at="" yahoo.com=""> wrote: > Dear All, > > I normalised and summarised my data using gcrma() routine and have the > expression values for each probeset. I now want to do the comparison between two > classes of the samples (i.e. fold change between the classes). One thing I'm not > sure is how to compare them because, as I read from the gcrma paper, the > expression values after the gcrma() routine are log(intensity) after background > adjustment. > > My question is: Do I have to convert the expression values from gcrma() back to > raw values by e^(values) before calculate the fold change between the two > classes that I have? > > Best > > Yot > > _______________________________________________ > 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 > -- Successful people ask better questions, and as a result, they get better answers. (Tony Robbins)