Dear All: Recently I did some Ambion bioarray (one color hybridization), and got data of 6 arrays in 3 gpr files(in each gpr file there will be two array which being designated as block1 and block 2)from GenePix. I am having trouble to normalize my data. Can anyone kindly give me any clue? Thanks a lot! Qingping Cui Albert Einstein Cancer Center

I am not familiar with Ambion but you could use quantile normalization if it seems reasonable. Also, look to see what methods are used for Codelink arrays. --Naomi At 01:30 PM 12/7/2006, julin at aecom.yu.edu wrote: >Dear All: > >Recently I did some Ambion bioarray (one color hybridization), and got >data of 6 arrays in 3 gpr files(in each gpr file there will be two array >which being designated as block1 and block 2)from GenePix. I am having >trouble to normalize my data. Can anyone kindly give me any clue? >Thanks a lot! > >Qingping Cui >Albert Einstein Cancer Center > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

Hi, A suggestion might be to have a look at the replicate spacing; from the only Ambion arrays I have tried to analyse, they "helpfully" have the control blocks as "top left" and "bottom right" on each slide, so the top array layout is NOT the same as the bottom array layout within each gpr. So, when you define spacing = x within limma, none of the duplicates actually "line up" with each other, assuming you are wanting to treat the two duplicates on each slide in this way. I got around it by reordering the second half of gpr file to give a constant spacing, then proceeding as usual with limma. HTH, al > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > julin at aecom.yu.edu > Sent: 07 December 2006 18:30 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Help:How to do normalization with Ambion > bioarray data? > > > Dear All: > > Recently I did some Ambion bioarray (one color > hybridization), and got data of 6 arrays in 3 gpr files(in > each gpr file there will be two array which being designated > as block1 and block 2)from GenePix. I am having trouble to > normalize my data. Can anyone kindly give me any clue? Thanks a lot! > > Qingping Cui > Albert Einstein Cancer Center > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/biocondu> ctor > Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >