HuEx 1.0 st v2 Two replicates each at 0h 3h 6h 12h 24h 48h I've extracted my summarized data from aroma.affymetrix as a data frame, I now need to import it into limma and normalize to the 0h time point. My ultimate goal is to return a gene list and heatmap that pass my filters, say p<=.05 and fc>=1.5 My main question however, is if there is a function in limma or any other package that will perform this normalization to the 0h time point and create ratios of the form (Time x)/(time 0) Thank you Ray [[alternative HTML version deleted]]

Hi Ray, I noticed Ken Simpson's reply to your post on the aroma.affymetrix mailing list; specifically his suggestion of "You could define contrasts (t3-t0, t6- t0, t12-t0, t24-t0, t48-t0) " is a good one. You'll need to check the very comprehensive limma user guide if this means nothing to you. library(limma) limmaUsersGuide() Once you've gone through this and worked through examples, then post back if you still have problems. cheers, Mark ----------------------------------------------------- Mark Cowley, BSc (Bioinformatics)(Hons) Peter Wills Bioinformatics Centre Garvan Institute of Medical Research ----------------------------------------------------- On 26/06/2008, at 2:12 AM, Roberts, Raymond wrote: > HuEx 1.0 st v2 > > Two replicates each at 0h 3h 6h 12h 24h 48h > > > > > > I've extracted my summarized data from aroma.affymetrix as a data > frame, > I now need to import it into limma and normalize to the 0h time point. > My ultimate goal is to return a gene list and heatmap that pass my > filters, say p<=.05 and fc>=1.5 > > > > My main question however, is if there is a function in limma or any > other package that will perform this normalization to the 0h time > point > and create ratios of the form > > (Time x)/(time 0) > > > > Thank you > > Ray > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor