search for: samplenames

Hello List. I have many files of ECG, each one with 7 column and I need only the second column and the name of each ECG. I am doing this but althought I have various days trying this i haven't gotten, so I ask help with this, if somebody cans help me I'll be so thankfully. --------------------------------------------------------------------------------------------------------

Hello R-friends, i have a question to the "text"-function. a little test-dataset for better understanding: -the dataset was imported with read.table(....,header=TRUE) s1-s10 are the samplenames var1 var2 var3 s1 1 1 2 s2 2 3 1 s3 2 2 3 s4 5 4 3 s5 4 2 3 s6 6 3 2 s7 8 5 4 s8 7 2 1 s9 9 3 2 s10 8 6 4 -then i??ve performed a pincipal component analysis with prcomp -for displaying the re...

Hi, The following command: axis(1, at= 1:50, labels= sampleNames(data)) produces an X-axis with 50 ticks and labels drawn from the sampleNames namespace. Problem is the labels at each tick are printed parallel to the x-axis and thus run into each other. How do I specify for the labels to be printed perpendicular to the x-axis? Thanks in advance. Anjan -- =====...

...e.001', 'income.002') sapply(filenames,function(x) { save( list=x , file = paste(x ,'.r', sep ='') ) }) rm(sat.001,sat.002,income.001,income.002,filenames) ls() # ############## #my for loop divide = function(x,y) {x/y} #creates a custom function #inputs to my loop: samplenames=c('001','002') x.name='sat' y.name='income' fun='divide' for (i in 1:length(samplenames) ) { x.name.suf = paste(x.name,samplenames[i],sep='.') #name of x file on hrd drive y.name.suf = paste(y.name,samplenames[i],sep='.') #name of y file...

...ss() to see what the object is. str() / attributes() to probe inside the object, and something@something$something to walk it and explore. Is there any other way? Also, without reading documentations, is there a way to know what functions are available to extract data from it? For example, there is sampleNames() which works on ExpressionSet and AnnotatedDataFrame (which is a part of ExpressionSet). How do I know they are available (as sometimes I can't recall where I've seen them and I forgot the function names). And what are R functions? Are those two separate functions or polymorphic functions?...

...<- paste(processedDir,"/",strInputAccession,"_default_exprs.csv",sep="") if(file.exists(sampleFile)){ affyobj <- try(ReadAffy(filenames=read.table(sampleFile,as.is =T,header=FALSE)[,1])) if(class(affyobj)=="try-error"){ rm(affyobj) }else{ sampleNames(affyobj) <- sub("\\..*","",sampleNames(affyobj)) #get rid of .CEL etc extension, just keep GSM } } if(!exists("affyobj")){ mdExprs <- as.matrix(read.csv(defaultExprs,row.names=1)) if( min( mdExprs, na.rm = TRUE ) >= 0 & max( mdExprs, na.rm = TRUE )...

Hi all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of "datadir" i have to mention the character string of the directory of these .cel files. I don't know how to give the path for all these files. i set the path as given below, > rna....

...png(paste(savepath,"a_rnaplot.png",sep = ""),width = fwidth, height = fheight,pointsize = fpointsize); data_deg <- AffyRNAdeg(data_cel) plotAffyRNAdeg(data_deg,col=cols,lty=1,lwd = "2") #a <- par("fin") legend("bottomright",sampleNames(data_cel),col=cols,lty=1) RNAdegSlope = cbind("Sample Names" = data_deg$sample.names, "RNA Deg Slope" = data_deg$slope) write.csv(RNAdegSlope, file = paste(savepath,"RNAdegSlope.csv",sep = "")) dev.off() I got this error message: Error in X11...

..... .. .. ..$ f.u : chr [1:128] "BMT / DEATH IN CR" "REL" "REL" "REL" ... > .. .. .. ..$ date last seen: chr [1:128] NA "8/28/2000" "10/15/1999" "1/23/1998" ... > .. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns" > .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots > .. .. .. .. ..@ .Data:List of 1 > .. .. .. .. .. ..$ : int [1:3] 1 1 0 > ..@ featureData :Formal class 'AnnotatedDataFrame' [pa...

...matchSigLength at line 603. The context for this is the thread starting at https://stat.ethz.ch/pipermail/bioconductor/2012-August/047241.html where a complicated package dependency and attempt to redefine an existing method leads to Error : package slot missing from signature for generic 'sampleNames<-' and classes LumiBatch, ANY cannot use with duplicate class names (the package may need to be re-installed) Martin -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2...

...2cdf.qcdef to the cirectory: ../R/x86_64-pc-linux-gnu-library/2.12/simpleaffy/extdata/drosgenome2cdf.qcdef I than try to run the analysis again: > data <- ReadAffy() > data AffyBatch (storageMode: lockedEnvironment) assayData: NA features, NA samples element names: exprs protocolData sampleNames: 10_w1h_021110.CEL 11_wbh_021110.CEL ... 9_dch_021110.CEL (12 total) varLabels: ScanDate varMetadata: labelDescription phenoData sampleNames: 10_w1h_021110.CEL 11_wbh_021110.CEL ... 9_dch_021110.CEL (12 total) varLabels: sample varMetadata: labelDescription featureData: none exper...

...blem is in the way I have specified dependencies in NAMESPACE or DESCRIPTION. It appears that dependecies need to be specified in both. These two files are shown below. ------------------------------ NAMESPACE export(nv.batch.normalize, norm.options, combine.norm.esets, subset.norm.eset, update.sampleNames) import(affy, simpleaffy, hgu133acdf, hgu133plus2cdf) importFrom(affyio, read.celfile, read.celfile.header) DESCRIPTION ... Depends: R (>= 2.5.0), Biobase Imports: affy, affyio, simpleaffy, hgu133acdf, hgu133plus2cdf -------------------------------- I'd appreciate any help. Thank you....

...prs.csv",sep="") >> >> if(file.exists(sampleFile)){ >> affyobj<- try(ReadAffy(filenames=read.**table(sampleFile,as.is >> =T,header=FALSE)[,1])) >> if(class(affyobj)=="try-error"**){ >> rm(affyobj) >> }else{ >> sampleNames(affyobj)<- sub("\\..*","",sampleNames(**affyobj)) #get >> rid >> of .CEL etc extension, just keep GSM >> } >> } >> >> if(!exists("affyobj")){ >> mdExprs<- as.matrix(read.csv(**defaultExprs,row.names=1)) >> if...

...e files and installed in the directory /usr/lib64/R/library but when i try using those files, they show as not installed. Anybody encounter this problem before OR is there something else i am doing wrong? Following is the sequence of stpes i used first: 1) library(affy) 2) pcpc <- ReadAffy(sampleNames=c("107762","110662","110682","110792","110802","111301","111611","111781","111801","154272","160881")) 3) pc <- rma(pcpc) Error in library("hgu133plus2cdf", lib.loc = NULL,...

...e 0.94 Z Female Case 0.32 # now the sample use > (subset1 =subset(expressionSet,sex="Male",type="Control")) 7 columns selected (C F J R U W X) ExpressionSet (storageMode: lockedEnvironment) assayData: 500 features, 7 samples element names: exprs, se.exprs phenoData sampleNames: C, F, ..., X (7 total) varLabels and varMetadata description: sex: Female/Male type: Case/Control score: Testing Score featureData featureNames: AFFX-MurIL2_at, AFFX-MurIL10_at, ..., 31739_at (500 total) fvarLabels and fvarMetadata description: none experimentData: use 'exp...

hey, i am using the flickr wrapper for ruby and need to access the tags of a specific photo. i got all the rest working. i must admit i am kind of new to ruby, but i tried and tried and couldn''t figure it out. among other things i want to read geotags like in my example here: http://www.flickr.com/photos/whoisstan/146634506/ i''m sure it is deadsimple and i just overlooked it.

Hi, This is a question of a newbie getting into the exciting world of R. I have several dataframes in the same format as NAD: > NAD[1:3,1:3] Sample.Id Main.abs..1 Main.abs..2 148 10a 0.04836 0.04994 167 11a_1109 0.32245 0.36541 173 11b_1109 0.29293 0.32815 What I want to do is to replace the Sample.Id with a corresponding number.The number