search for: exprdata

...conductor.org/biocLite.R") biocLite() library(limma) library(Biobase) #change directory to folder where files are (c:/limmadegenes) #Change to directory with original data files #read in expression data file and phenotypic data. #Note that row.names=1 means that row names are #in column 1, exprdata<-read.table("exprsData.txt", header=TRUE,sep="\t",row.names=1,as.is=TRUE,fill=TRUE,) class(exprdata) #[1] "data.frame" dim(exprdata) #[1] 17328 28 colnames(exprdata) head(exprdata) #printout too long to paste phenotypicdata<-read.table("phenotypicdata.txt...

Hi all, I have two question. First, I wonder how to remove a part of the column names in a matrix? I would like to remove the "_ACCX" or "_NAX" part below. Is there a method where the "_" as well as all characters after i can be removed? > dim(exprdata) [1] 88 512 > > colnames(exprdata[,c(1:20)]) [1] "Akita_ACC1" "Akita_ACC2" "Akita_ACC3" "Akita_ACC4" "Alc.0_ACC1" "Alc.0_ACC2" "Alc.0_ACC3" [8] "Alc.0_ACC4" "Alc.0_ACC5" "Bl.1_ACC1" &quot...

...s, and I am not experienced enough with R to know how it stores data when looping and how to overcome this problem. By having it print the avg, I was expecting to see 24 numbers, but it only gives me one. Here is my code. cts.sds<-array(1:24,c(3,8)) for(i in 3){ for(j in 8){ avg<-sum(exprdata[3*i-2:3*i,j]/3) cts.sds[i,j]<-avg print(avg) } } print(cts.sds) Any help with this pesky matter will be greatly appreciated. -- View this message in context: http://www.nabble.com/Help-with-loops-and-how-R-stores-data-tp15247392p15247392.html Sent from the R help mailing list archi...

Hi all, I would like to remove rows from a matrix, based on the frequency of missing values. If there are more than 10 % missing values, the row should be deleted. I use the following to calculate the frequencies, thereby getting a new matrix with the frequencies: freqNA=rowMeans(is.na(exprdata)) But is there a shorter way to remove the rows based on "(1-freqNA)>0.1" than looping through the whole matrix using a for loop? All the best, Joel _________________________________________________________________ Hitta kärleken i vinter! http://dejting.se....