Your understanding of what the code is doing is correct. eg > data(affybatch.example) > pm(affybatch.example)[1,] 20A 20B 10A 149 118 124 > pm(affybatch.example)[1,1] <- NA > affybatch.example.norm <- normalize(affybatch.example) > pm(affybatch.example)[1:3,] 20A 20B 10A [1,] NA 118.0 124.0 [2,] 143.5 124.8 116.5 [3,] 132.0 111.0 105.0 > pm(affybatch.example.norm)[1:3,] 20A 20B 10A [1,] NA 118.0000 124.0000 [2,] 127.2667 137.3667 120.1667 [3,] 115.8333 122.6000 107.3333 > Note that normalize calls normalize.AffyBatch.quantiles by default in this case. Why does it do this? Because the underlying routine which does the normalization normalize.quantiles() does not handle NA values. In some sense this was done by design, the thinking being that if you start off with raw CEL file data there should not be any missing data. Ben On Fri, 2006-06-30 at 09:33 -0500, odlc at uchicago.edu wrote: > Hello, > > I am trying to understand how normalize.AffyBatch.quantiles > works. From what I understand of the code, it seems that > rows (corresponding to a probe) which contain even a single > NA are dropped; then, the quantile-normalization method > described in Botstein et al. is applied to the remaining rows, > and these normalized rows are put back into the original > batch. > > In other words, values in a row that contains NA's > remain unchanged. > > Questions: > > - Is this really how it works? > > - If yes, is this the intended behavior? > > Thank you, > > Omar. > > _______________________________________________ > 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 -- Ben Bolstad <bmb at="" bmbolstad.com=""> http://bmbolstad.com

Ben, Thank you very much for the answer. By the way, I got your name wrong in my posting. For the record, for those who might read this: the correct reference for the quantile normalization procedure for microarrays is: Bolstad et al., Bioinformatics, 19(2):185?193, Jan 2003 Sorry for the confusion, Omar. ---- Original message ---- >Date: Wed, 05 Jul 2006 09:16:08 -0700 >From: Ben Bolstad <bmb at="" bmbolstad.com=""> >Subject: Re: [BioC] normalize.AffyBatch.quantiles and NA values >To: odlc at uchicago.edu >Cc: bioconductor at stat.math.ethz.ch > >Your understanding of what the code is doing is correct. eg > >> data(affybatch.example) >> pm(affybatch.example)[1,] >20A 20B 10A >149 118 124 >> pm(affybatch.example)[1,1] <- NA >> affybatch.example.norm <- normalize(affybatch.example) >> pm(affybatch.example)[1:3,] > 20A 20B 10A >[1,] NA 118.0 124.0 >[2,] 143.5 124.8 116.5 >[3,] 132.0 111.0 105.0 >> pm(affybatch.example.norm)[1:3,] > 20A 20B 10A >[1,] NA 118.0000 124.0000 >[2,] 127.2667 137.3667 120.1667 >[3,] 115.8333 122.6000 107.3333 >> > > >Note that normalize calls normalize.AffyBatch.quantiles by default in >this case. > >Why does it do this? Because the underlying routine which does the >normalization normalize.quantiles() does not handle NA values. In some >sense this was done by design, the thinking being that if you start off >with raw CEL file data there should not be any missing data. > > >Ben > > >On Fri, 2006-06-30 at 09:33 -0500, odlc at uchicago.edu wrote: >> Hello, >> >> I am trying to understand how normalize.AffyBatch.quantiles >> works. From what I understand of the code, it seems that >> rows (corresponding to a probe) which contain even a single >> NA are dropped; then, the quantile-normalization method >> described in Botstein et al. is applied to the remaining rows, >> and these normalized rows are put back into the original >> batch. >> >> In other words, values in a row that contains NA's >> remain unchanged. >> >> Questions: >> >> - Is this really how it works? >> >> - If yes, is this the intended behavior? >> >> Thank you, >> >> Omar. >> >> _______________________________________________ >> 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 >-- >Ben Bolstad <bmb at="" bmbolstad.com=""> >http://bmbolstad.com >