Dear Henrick, Wish you had a wonderful holiday season and thank for answering my questions. I have two questions to you. 1. Based on my reading to the information about the aroma.affymetrix, it is designed for analyzing SNP array data. Do you think it will be ok for my case since I need to normalize HG-u133_Plus2 expression array using dChip with a specific array as median array? 2. I have created the annotationData/chipTypes/... and rowData/test_2009/E10252_U133Plus2.cel ... folders. When I was trying to run the following script: cs <- AffymetrixCelSet$byName(name, tags, chipType="HG-U133_Plus_2") I received a error message saying: "Error in getVector.Arguments(static, s, length = length, .name = .name) : object "name" not found" my question to you is that how I can define the name object? As a file named name I appreciate your help! Aiguo -----Original Message----- From: Henrik Bengtsson [mailto:hb@stat.berkeley.edu] Sent: Monday, December 29, 2008 10:54 AM To: Li, Aiguo (NIH/NCI) [E] Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Does any one know a package that allow command line dChip normalization with a specific median array? Hi, aroma.affymetrix can do this: library("aroma.affymetrix"); csR <- AffymetrixCelSet$byName("MyDataSet", chipType="HG- U133_Plus_2"); cfT <- getFile(csR, 14); # Normalize toward array #14 (say) qn <- QuantileNormalization(csR, targetDistribution=cfT); csN <- process(qn); For further question, please join the aroma.affymetrix mailinglist [http://www.braju.com/R/aroma.affymetrix/]. Cheers Henrik On Wed, Dec 24, 2008 at 4:15 PM, Li, Aiguo (NIH/NCI) [E] <liai at="" mail.nih.gov=""> wrote: > Hello all, > > > > I need to normalize expression array from command line using a specific > array as baseline median array. Does anybody know a package that allows > me to do that? I have checked the expresso package and think that it > does not allow me to specify a specific array as median array. > > > > Thanks and have great holiday! > > > > AG Lee > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >

Hi. On Mon, Jan 5, 2009 at 8:33 PM, Li, Aiguo (NIH/NCI) [E] <liai at="" mail.nih.gov=""> wrote: > Dear Henrick, > > Wish you had a wonderful holiday season and thank for answering my > questions. I have two questions to you. > > 1. Based on my reading to the information about the aroma.affymetrix, > it is designed for analyzing SNP array data. Do you think it will be ok > for my case since I need to normalize HG-u133_Plus2 expression array > using dChip with a specific array as median array? No, it is not for SNP chips only. That's been my main field so it has naturally methods for those chip types, but as more developers joined we now support almost all Affymetrix chip types. Please see the list of features on the webpage and the vignettes for other examples. To get exact dChip performance, you'll need to use the dChip software (http://www.dchip.org/ - note that they have a new forum with links to Linux ports as well). I've tried to imitate the dChip normalization and summarization steps, but I never managed to replicate the results exactly using R, BioC, etc. > > 2. I have created the annotationData/chipTypes/... and > rowData/test_2009/E10252_U133Plus2.cel ... folders. When I was trying > to run the following script: > cs <- AffymetrixCelSet$byName(name, tags, chipType="HG-U133_Plus_2") > I received a error message saying: "Error in getVector.Arguments(static, > s, length = length, .name = .name) : > object "name" not found" > my question to you is that how I can define the name object? As a file > named name Your setup as written above is not correct. Pay close attention to the examples as this is described very carefully and I hope clearly and unambiguously. I also recommend you to start reading the User's Guide: http://groups.google.com/group/aroma-affymetrix/web/users-guide Please post further questions related to aroma.affymetrix to the aroma.affymetrix mailing list (this is the BioC list). Cheers /Henrik > > I appreciate your help! > > Aiguo > > -----Original Message----- > From: Henrik Bengtsson [mailto:hb at stat.berkeley.edu] > Sent: Monday, December 29, 2008 10:54 AM > To: Li, Aiguo (NIH/NCI) [E] > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Does any one know a package that allow command line > dChip normalization with a specific median array? > > Hi, > > aroma.affymetrix can do this: > > library("aroma.affymetrix"); > csR <- AffymetrixCelSet$byName("MyDataSet", chipType="HG- U133_Plus_2"); > cfT <- getFile(csR, 14); # Normalize toward array #14 (say) > qn <- QuantileNormalization(csR, targetDistribution=cfT); > csN <- process(qn); > > For further question, please join the aroma.affymetrix mailinglist > [http://www.braju.com/R/aroma.affymetrix/]. > > Cheers > > Henrik > > On Wed, Dec 24, 2008 at 4:15 PM, Li, Aiguo (NIH/NCI) [E] > <liai at="" mail.nih.gov=""> wrote: >> Hello all, >> >> >> >> I need to normalize expression array from command line using a > specific >> array as baseline median array. Does anybody know a package that > allows >> me to do that? I have checked the expresso package and think that it >> does not allow me to specify a specific array as median array. >> >> >> >> Thanks and have great holiday! >> >> >> >> AG Lee >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> >