Hi. On Tue, Apr 5, 2011 at 2:41 PM, xiaowei guan <xwei.g...@gmail.com> wrote: > Dear All, > > Currently I am analyzing the affyU133 plus 2.0 data. I downloaded the > raw data in .CEL format and I would like to derive the gene centric > values just for one gene, which means collapse the values of a probe > set that corresponding to a gene in to a summary value for that gene. > which command in aroma.affymetrix can fulfill this task?
Yes, this is classical Affymetrix probe summarization. Methods such as RMA (a sequence of steps) will provide you with gene summaries, cf. http://aroma-project.org/vignettes/. It is the Affymetrix Chip Definition File (CDF) that defines what probes constitutes a gene and hence should be summarized together. > > Another question is that, if I download the CDF file from > affyprobeMiner, which format shall I use if I want to analyze it using > bioconductor? My machine is 64 bit, does that matter? > Please see the following link: > http://gauss.dbb.georgetown.edu/liblab/affyprobeminer/gene.html. > Which one exactly shall I download? > > After I download the CDF file I manually install it into R. while R > won't recognize it. There is some error message like: this folder has > been build a in the version lower than 2.10, re-install it? What does > this mean? This sounds like a question to the Bioconductor mailing list, because it is unrelated to the aroma.affymetrix framework. Please ask for help there. Also, beware that the term CDF is often misused in a way that it means something else than the Affymetrix CDF file with filename ending *.CDF. In Bioconductor the term "CDF" is often used when it should be "CDF package" or "CDF environment", cf. the notes on http://aroma-project.org/definitions/chipTypesAndCDFs Hope this helps Henrik > > Thanks a lot for your help. Appreciate it. > > best, > Xiaowei > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
