Dear Jim Sorry I didn't mean to hold back but do not quite understand what to say - please see below. I tried two different approaches - 1) install ecoliasv2cdf available as a Bioconductor package and 2) rmove the Bioconductor package and install the cdf library I downloaded from Affy's website using "make.cdf.package" and "R CMD INSTALL". When I type the following commands after restarting the R GUI: > library(affy) > setwd("<path-to-cel-files>") > eset <- justRMA(cdfname = "ecoliasv2cdf") At this point R crashes. I tried waiting for up to 10 min before force-quitting R. I also tried the following: > library(affy) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > setwd("<path-2-cel-files>") > data<-ReadAffy(cdfname="ecoliasv2cdf") Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : Cel file //xyz.CEL does not seem to be of Ecoli_antisense type > I am doing this in R 2.9.0 installed on an Apple Intel Core Duo machine running OS X Leopard 10.5.8. If you need more information pl. do let me know. Thank you for trying to help me. BALA On Wed, Mar 17, 2010 at 3:48 PM, James MacDonald <jmacdon@med.umich.edu>wrote: > Please don't take things off-list. The list archives are considered a > resource for others to search for answers. > > > Balasubramanian Ganesan wrote: > >> Hi Jim >> This doesn't seem to help. >> Any other suggestions? >> > > You're going to have to give more input than that. What happens? What > exactly did you do? Did you try installing the ecoliasv2cdf first? > > Best, > > Jim > > > Thanks >> BALA >> >> >> On Wed, Mar 17, 2010 at 10:06 AM, James W. MacDonald < >> jmacdon@med.umich.edu <mailto:jmacdon@med.umich.edu>> wrote: >> >> Hi Bala, >> >> Try this: >> >> eset <- justRMA(cdfname = "ecoliasv2cdf") >> >> Best, >> >> Jim >> >> >> >> Balasubramanian Ganesan wrote: >> >> Hello BioC team >> I have downloaded an old microarray expression data set for >> analysis from >> NCBI's GEO database. >> When I try to normalize the data in R2.9 (OS X Leopard) using >> justRMA() the >> normalization fails as it is looking for a library file called >> "ecoliantisensecdf" >> and cannot find it. >> However if try to download the corresponding library file from >> Affy''s >> website I only get a library file called "Ecoli_ASv2" and not >> "ecoliantisense". >> Affymetrix insists that this library file works fine with the >> cel files I >> have inside their software (Expression console) and that the >> array layouts >> of the older ecoliantisense and the newer Ecoli_ASv2 are the >> same. But I >> have had no luck trying to use the new library in R. >> Is there a possible way to resolve this issue? >> Thank you inn advance. >> BALA >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> <mailto:bioconductor@stat.math.ethz.ch> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues >> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > Hildebrandt Lab > 8220D MSRB III > 1150 W. Medical Center Drive > Ann Arbor MI 48109-5646 > 734-936-8662 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > [[alternative HTML version deleted]]

Dear Jim Sorry, I did not quite understand your earlier comment and had no specific intention of getting things off the mailing list - probably a reflex to just hit "reply" instead of "reply all". My apologies to you and other list members. Just a note that as to why I misunderstood your earlier comment - it didn't address me, as I saw it. About the chips: ah, sorry. This is something I have done earlier for a different chip with two diff. cdf libraries but I never realized that this issue was causing the troubles. Thanks for bringing this to my attention. BALA On Mon, Mar 22, 2010 at 12:27 PM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Bala, > > Again. Please don't take things off list. In other words, you shouldn't be > responding to me alone. Instead, respond to all so our conversation goes > back to the list. The whole purpose of this list is to be a repository of > information that people can use to answer questions themselves. If you keep > taking things off list, then this cannot be of any help to people in the > future. > > Balasubramanian Ganesan wrote: > >> Hi Jim >> >> It is GSE 7398. >> Here's the link to it below. >> BALA >> >> http://www.ncbi.nlm.nih.gov/gds/?term=GSE7398 >> > > > The problem with these chips is that they are a mixture of EcoliASv2 and > Ecoliantisense chips, so you will have to process them separately. > > First, let's look at what the chips are: > > > lst2 <- lapply(lst, affyio:::read.celfile.header) > > names(lst2) <- list.celfiles() > > sapply(lst2, function(x) x[1]) > $GSM177549.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177550.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177551.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177552.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177553.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177554.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177555.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177556.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177557.CEL.cdfName > [1] "Ecoli_ASv2" > > $GSM177558.CEL.cdfName > [1] "Ecoli_ASv2" > > $GSM177559.CEL.cdfName > [1] "Ecoli_ASv2" > > $GSM177560.CEL.cdfName > [1] "Ecoli_ASv2" > > $GSM177561.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177562.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177563.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177564.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177565.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177566.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177567.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177568.CEL.cdfName > [1] "Ecoli_antisense" > > $GSM177569.CEL.cdfName > [1] "Ecoli_ASv2" > > $GSM177570.CEL.cdfName > [1] "Ecoli_ASv2" > > $GSM177571.CEL.cdfName > [1] "Ecoli_ASv2" > > $GSM177572.CEL.cdfName > [1] "Ecoli_ASv2" > > Now make an index to separate the two chip types > > > > ind1 <- which(sapply(lst2, function(x) x[1]) == "Ecoli_ASv2") > > ind1 > GSM177557.CEL.cdfName GSM177558.CEL.cdfName GSM177559.CEL.cdfName > 9 10 11 > GSM177560.CEL.cdfName GSM177569.CEL.cdfName GSM177570.CEL.cdfName > 12 21 22 > GSM177571.CEL.cdfName GSM177572.CEL.cdfName > 23 24 > > And process each type separately: > > > eset1 <- justRMA(filenames=list.celfiles()[ind1], > cdfname="ecoliantisensecdf") > > eset2 <- justRMA(filenames=list.celfiles()[-ind1]) > > > Best, > > Jim > > > >> >> On Mon, Mar 22, 2010 at 9:47 AM, James W. MacDonald < >> jmacdon@med.umich.edu <mailto:jmacdon@med.umich.edu>> wrote: >> >> Hi Bala, >> >> What GEO dataset are you using? >> >> Jim >> >> >> >> Balasubramanian Ganesan wrote: >> >> Dear Jim >> Sorry I didn't mean to hold back but do not quite understand >> what to say - please see below. >> I tried two different approaches - 1) install ecoliasv2cdf >> available as a Bioconductor package and 2) rmove the >> Bioconductor package and install the cdf library I downloaded >> from Affy's website using "make.cdf.package" and "R CMD INSTALL". >> When I type the following commands after restarting the R GUI: >> > library(affy) >> > setwd("<path-to-cel-files>") >> > eset <- justRMA(cdfname = "ecoliasv2cdf") >> >> At this point R crashes. I tried waiting for up to 10 min before >> force-quitting R. >> I also tried the following: >> > library(affy) >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> > setwd("<path-2-cel-files>") >> > data<-ReadAffy(cdfname="ecoliasv2cdf") >> Error in read.affybatch(filenames = l$filenames, phenoData = >> l$phenoData, : Cel file //xyz.CEL does not seem to be >> of Ecoli_antisense type >> > >> I am doing this in R 2.9.0 installed on an Apple Intel Core Duo >> machine running OS X Leopard 10.5.8. >> If you need more information pl. do let me know. >> Thank you for trying to help me. >> BALA >> >> On Wed, Mar 17, 2010 at 3:48 PM, James MacDonald >> <jmacdon@med.umich.edu <mailto:jmacdon@med.umich.edu=""> >> <mailto:jmacdon@med.umich.edu <mailto:jmacdon@med.umich.edu="">>> >> wrote: >> >> Please don't take things off-list. The list archives are >> considered >> a resource for others to search for answers. >> >> >> Balasubramanian Ganesan wrote: >> >> Hi Jim >> This doesn't seem to help. >> Any other suggestions? >> >> >> You're going to have to give more input than that. What happens? >> What exactly did you do? Did you try installing the >> ecoliasv2cdf first? >> >> Best, >> >> Jim >> >> >> Thanks >> BALA >> >> >> On Wed, Mar 17, 2010 at 10:06 AM, James W. MacDonald >> <jmacdon@med.umich.edu <mailto:jmacdon@med.umich.edu=""> >> <mailto:jmacdon@med.umich.edu <mailto:jmacdon@med.umich.edu="">> >> <mailto:jmacdon@med.umich.edu>> <mailto:jmacdon@med.umich.edu> <mailto:jmacdon@med.umich.edu>> <mailto:jmacdon@med.umich.edu>>>> >> >> wrote: >> >> Hi Bala, >> >> Try this: >> >> eset <- justRMA(cdfname = "ecoliasv2cdf") >> >> Best, >> >> Jim >> >> >> >> Balasubramanian Ganesan wrote: >> >> Hello BioC team >> I have downloaded an old microarray expression >> data set for >> analysis from >> NCBI's GEO database. >> When I try to normalize the data in R2.9 (OS X >> Leopard) using >> justRMA() the >> normalization fails as it is looking for a library >> file >> called >> "ecoliantisensecdf" >> and cannot find it. >> However if try to download the corresponding >> library file >> from >> Affy''s >> website I only get a library file called >> "Ecoli_ASv2" and not >> "ecoliantisense". >> Affymetrix insists that this library file works >> fine with the >> cel files I >> have inside their software (Expression console) >> and that the >> array layouts >> of the older ecoliantisense and the newer >> Ecoli_ASv2 are the >> same. But I >> have had no luck trying to use the new library in R. >> Is there a possible way to resolve this issue? >> Thank you inn advance. >> BALA >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> <mailto:bioconductor@stat.math.ethz.ch> >> <mailto:bioconductor@stat.math.ethz.ch>> <mailto:bioconductor@stat.math.ethz.ch>> >> <mailto:bioconductor@stat.math.ethz.ch>> <mailto:bioconductor@stat.math.ethz.ch> >> <mailto:bioconductor@stat.math.ethz.ch>> <mailto:bioconductor@stat.math.ethz.ch>>> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every >> day, and >> should >> not be used for urgent or sensitive issues >> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> Hildebrandt Lab >> 8220D MSRB III >> 1150 W. Medical Center Drive >> Ann Arbor MI 48109-5646 >> 734-936-8662 >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and >> should >> not be used for urgent or sensitive issues >> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues >> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > [[alternative HTML version deleted]]