that's ok, but i am afraid that these 3 biological replicates differ to much (three different patients), so that i loose some information when normalizing them all togehter. i think also that the best way to normalize them is to normalizing them all together with RMA. what replicates are you using? technical or biological? you are analyzing 2 replicates exposed to 6 different treatments? Quoting Naomi Altman <naomi@stat.psu.edu>: > There may be problems with only 3 arrays. But there should not be a > problem with 3 replicates for 3 times = 9 arrays. We used RMA on 2 > replicates for 6 treatments = 12 arrays, and the results seemed fine. > > --Naomi > > At 03:28 PM 7/29/2004 +0100, Adaikalavan Ramasamy wrote: > >Perhaps. But my main concern with performing RMA on patient by patient > >is that the difference between patients could possibly be confounded > >with normalisation. i.e. You cannot tell if an observed difference is > >due to patient difference or due to normalisation. > > > >The other problem with doing that is that you only have 3 chips. The > >following thread is almost a year old but it indicates possible problems > >with only 3 chips. > > http://files.protsuggest.org/biocond/html/3346.html > > > >Regards, Adai. > > > >On Thu, 2004-07-29 at 15:13, Dipl.-Ing. Johannes Rainer wrote: > > > ok, > > > normalizing all together because of the better model parameter fitting? > > > > > > > > > > > > Quoting Stephen Henderson <s.henderson@ucl.ac.uk>: > > > > > > > all together. > > > > > > > > -----Original Message----- > > > > From: Dipl.-Ing. Johannes Rainer > > > > To: bioconductor@stat.math.ethz.ch > > > > Sent: 7/29/04 2:22 PM > > > > Subject: [BioC] RMA with biological replicates > > > > > > > > hi, > > > > > > > > i have again a question about RMA and how it works with a different > > > > number of > > > > chips. > > > > we are looking at the response of patients to a specific treatment, so > > > > we got > > > > biological replicates and no technical ones (as we have not enough > > > > material > > > > from the patients). at the moment i got 9 chips, 3 patients, 3 time > > > > points for > > > > each patient. > > > > What is now the best way to normalize them? normalize them all together > > > > with > > > > RMA, or normalize the chips from each patient separatly (that means > > > > normalize > > > > the 3 chips from patient one together, then those from patient 2...)? > > > > As i think, RMA gives better results if i have more chips to normalize > > > > together > > > > (more chips with roughly the same expression result in better fitted > > > > model > > > > parameters i guess). > > > > has anyone a conclusion what's the best was? > > > > > > > > thanks, jo > > > > > > > > _______________________________________________ > > > > Bioconductor mailing list > > > > Bioconductor@stat.math.ethz.ch > > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > > > > > ********************************************************************** > > > > This email and any files transmitted with it are confidential and > > > > intended solely for the use of the individual or entity to whom they > > > > are addressed. If you have received this email in error please notify > > > > the system manager (it.support@wibr.ucl.ac.uk). All files are scanned > for > > > > viruses. > > > > ********************************************************************** > > > > > > > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Bioinformatics Consulting Center > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > >