[R] limma function problem
Hi, I have two data set of normalized Affymetrix CEL files, wild type vs Control type.(each set have further three replicates). > wild.fish AffyBatch object size of arrays=712x712 features (10 kb) cdf=Zebrafish (15617 affyids) number of samples=3 number of genes=15617 annotation=zebrafish notes= > Dicer.fish AffyBatch object size of arrays=712x712 features (10 kb) cdf=Zebrafish (15617 affyids) number of samples=3 number of genes=15617 annotation=zebrafish notes= Now, I have to combine these two S4 objects and use lmFit function of Limma package.I am able to combine the two S4 objects using merge function. > merge.fish <-merge(wild.fish,Dicer.fish) > merge.fish AffyBatch object size of arrays=712x712 features (17833 kb) cdf=Zebrafish (15617 affyids) number of samples=6 number of genes=15617 annotation=zebrafish notes=Merge from two AffyBatches with notes: 1) , and 2) > design Wild Mz_Dicer GSM95623.CEL10 GSM95624.CEL10 GSM95625.CEL10 GSM95617.CEL01 GSM95618.CEL01 GSM95619.CEL01 > fit <-lmFit(merge.fish, design) Error in as.vector(data) : no method for coercing this S4 class to a vector > mode(merge.fish) [1] "S4" So, how to troubleshoot this problem? Regards, Sukhbir Singh Rattan. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] boxplot
Hi, I have simple query In which package drawBoxplot function is available? Regards, Sukhbir Singh Rattan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] creating R roll in Centos OS
Hi I have Centos Operating System. I m installing R on it. For this I have to create roll of R. So, how to create the roll of R, regarding this what to be downloaded and from where? Plz help. By Sukhbir Singh Rattan. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] boxplot
Hi, I m not able to plot normalized data(normalization by rma) using boxplot. I don't know why? basically, object(formed of normalized data) belong to ExpressionSet class. It is showing error Error in x[!xna] : object of type 'S4' is not subsettable In addition: Warning messages: 1: In is.na(x) : is.na() applied to non-(list or vector) of type 'S4' 2: In is.na(x) : is.na() applied to non-(list or vector) of type 'S4' Now, how to plot? Should I have use another function? By Sukhbir Singh Rattan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Annotation database
Hi, I have 15 CEL files of Affymetrix platform from GEO. Title of experiment is : Ecoli_ASv2 Affymetrix E. coli Antisense Genome Array. I am looking for the package available in R for this array for annotation. I have already tried doing annotation from packages like org.EcK12.eg.db but I don't got the success. Is any other package in the form of database available for E.coli for Annotation? By Sukhbir Singh Rattan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to set crontab for updating the repositories?
Hi, I have downloaded around 60GB package repositories of bioconductor to use it locally and to set up mirror at my university site. I have installed the mirror with rsync command and able to access also. Now I have to set a cron job for its daily updating from bioconductor website. How should I do it? I know rsync have to be used but I don't know the proper syntax. I request to send proper syntax. Thanks, Sukhbir Singh Rattan. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] .rda extension
Hi, I have very simple question. How to open/read/write the file with .rda extension which is usually available in the data folder of any package? By Sukhbir Singh Rattan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
