a) if you use expresso instead of the rma funciton i believe you get ad-hoc se estimtates. to extract them from the exprSet use the method se.exprs(). ben bolstad is working on improving the se estimate. basically by using rlm instead of the current ad-hoc procedure. b) not a concrete one. coding up what Affymetrix does is straight forward though. c) to the best of my knowledge, there wont be many differences between this release and the next. On Tue, 8 Apr 2003, Christian M. Probst wrote: > Hi, > > I am using the RMA function to analyze Genechip arrays. > > I would like to know if: > > a) There is an option to calculate the SE for the expression summary? > b) There is any plan to add a statistical test of gene status as in MAS 5.0 > (absent, present) using the background correct and only PM data. > c) What are the main implementations in Affy 1.2.9? > > Thanks in Advance > > Christian > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

a) if you use expresso instead of the rma funciton i believe you get ad-hoc se estimtates. to extract them from the exprSet use the method se.exprs(). ben bolstad is working on improving the se estimate. basically by using rlm instead of the current ad-hoc procedure. b) not a concrete one. coding up what Affymetrix does is straight forward though. c) to the best of my knowledge, there wont be many differences between this release and the next. On Tue, 8 Apr 2003, Christian M. Probst wrote: > Hi, > > I am using the RMA function to analyze Genechip arrays. > > I would like to know if: > > a) There is an option to calculate the SE for the expression summary? > b) There is any plan to add a statistical test of gene status as in MAS 5.0 > (absent, present) using the background correct and only PM data. > c) What are the main implementations in Affy 1.2.9? > > Thanks in Advance > > Christian > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

On Tue, Apr 08, 2003 at 09:31:19AM -0300, Christian M. Probst wrote: > c) What are the main implementations in Affy 1.2.9? You may refer to the file NEWS, found in the root of the package (although you may have to uncompress the pack you download to see it). I am not sure about how many new other things will come up, but probably not so many this time. We are working on cleaning the code and fixing the doc. For reference, this file currently contains: Version 1.2 [under development]: o Autoload of cdfenvs on demand [almost done. The packages directory on the website should be set to be a repository] o slot 'preprocessing' of the MIAME attribute used to store normalization step information [not finished, list returned "constant" and "invariantset" for the moment. Need for a class and check compliance with MIAME standards] o default methods for normalization, bg correction, pm correction and summary now in the package options [options exist for all, but only used by normalize for the moment]. o tuning of the MAS5.0 methods implemented (bgcorrect.mas, ...) [Ben for details. add URL for the comparison he made] o method plot.ProbeSet, an alternative to barplot, to plot probe level information. o parameter 'scale' in the method barplot for ProbeSet. All the barplots are scaled to eachothers. o bug in the parser fixed (infinite loop reported with apparently non-standard CEL files). o bug in the parser fixed (the 'sd' data returned were not correct). o missing slot in the dataset SpikeIn fixed. Hopin' it helps, Laurent -- -------------------------------------------------------------- currently at the National Yang-Ming University in Taipei, Taiwan -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent