Hi Henrik, Thanks for your suggestion. This package is just what we need. Shuli. On Tue, Jan 13, 2009 at 2:45 AM, Henrik Bengtsson <hb@stat.berkeley.edu>wrote: > More of a general help; have a look at the aroma.affymetrix package > > http://www.braju.com/R/aroma.affymetrix > > which doesn't have memory limits. > > /Henrik > > On Mon, Jan 12, 2009 at 7:43 AM, shuli kang <kangshuli@gmail.com> wrote: > > Hi, > > > > I'm using the normalize.scaling function in the affyPLM package to > normalize > > the data from several chips. By default, the argument "baseline" was set > as > > "-1". The document says negative values control different baseline > > selection methods: > > > > baseline Index of array to use as baseline, negative values (-1,-2,-3,-4) > > control different baseline selection methods > > > > But I can't find detailed description of these methods anywhere. Could > > anyone tell me what these methods are actually? > > > > PS: I'm dealing with plenty of chip data now. Usually I read all the CEL > > files at one time. However, I have to read them one by one if too many > CEL > > files involved, due to the limited physical memory . In such cases, I > tried > > to manually select the same reference array as the one selected by the > > default "baseline" values. So I want to know more about these reference > > selection methods. Of course, I could always choose the first array as > a > > reference. But this seems too arbitrary? > > > > Thanks in advance! > > > > Shuli. > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > [[alternative HTML version deleted]]

Hi Ben, So (-1,-2,-3,-4) equal to the "mean","median","pseudo-mean","pseudo- median" arguments used in other normalization methods. Thanks! Shuli. On Tue, Jan 13, 2009 at 12:26 PM, Ben Bolstad <bmb@bmbolstad.com> wrote: > Apologies for not having this documented anywhere and having not looked > at the code in way too long I had completely forgotten what these were > myself. But digging around in the C code: > > ** int baseline - index of array to be used as baseline. > ** this will be 0..cols-1, if it is > ** -1 pick array with median overall (total) intensity > as baseline > ** -2 pick array with median median as baseline > ** -3 generate a probewise median array for baseline > ** -4 generate a probewise mean array for baseline > > > Best, > > Ben > > > > On Mon, 2009-01-12 at 23:43 +0800, shuli kang wrote: > > Hi, > > > > I'm using the normalize.scaling function in the affyPLM package to > normalize > > the data from several chips. By default, the argument "baseline" was set > as > > "-1". The document says negative values control different baseline > > selection methods: > > > > baseline Index of array to use as baseline, negative values (-1,-2,-3,-4) > > control different baseline selection methods > > > > But I can't find detailed description of these methods anywhere. Could > > anyone tell me what these methods are actually? > > > > PS: I'm dealing with plenty of chip data now. Usually I read all the CEL > > files at one time. However, I have to read them one by one if too many > CEL > > files involved, due to the limited physical memory . In such cases, I > tried > > to manually select the same reference array as the one selected by the > > default "baseline" values. So I want to know more about these reference > > selection methods. Of course, I could always choose the first array as > a > > reference. But this seems too arbitrary? > > > > Thanks in advance! > > > > Shuli. > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]