What did your text files look like? It would appear that there was not a line feed on the last line of the file. Also what does 'str' of x and y show? It appears that one is a data frame and one is a matrix. That might be causing some of the problems.
On Nov 11, 2007 10:30 PM, affy snp <[EMAIL PROTECTED]> wrote: > Hi Jim, > > Thanks a lot! I am wondering why I ended up getting the result as follows: > > > x<-read.table(file="x.txt",header=TRUE,row.names=1,na.strings = "NA") > Warning message: > In read.table(file = "x.txt", header = TRUE, row.names = 1, na.strings = > "NA") : > incomplete final line found by readTableHeader on 'x.txt' > > x > b1 b2 b3 > a1 2 4 6 > a2 1 2 NA > a3 4 6 NA > > y<-as.matrix(read.table(file="y.txt",header=TRUE,row.names=1,na.strings = > > "NA")) > Warning message: > In read.table(file = "y.txt", header = TRUE, row.names = 1, na.strings = > "NA") : > incomplete final line found by readTableHeader on 'y.txt' > > y > b1 b2 b3 > a1 NA 4 4 > a2 2 2 NA > a3 1 2 2 > > z <- mapply(function(a,b)mean(c(a,b), na.rm=TRUE), x, y) > > z > b1 b2 b3 <NA> <NA> <NA> <NA> <NA> > 2.333333 3.500000 3.500000 2.750000 3.500000 4.000000 2.750000 4.000000 > <NA> > 4.000000 > > dim(z) <- dim(x) > > z > [,1] [,2] [,3] > [1,] 2.333333 2.75 2.75 > [2,] 3.500000 3.50 4.00 > [3,] 3.500000 4.00 4.00 > > is.na(z) <- is.nan(z) > > z > [,1] [,2] [,3] > [1,] 2.333333 2.75 2.75 > [2,] 3.500000 3.50 4.00 > [3,] 3.500000 4.00 4.00 > > > > > Allen > > > On Nov 11, 2007 5:27 PM, jim holtman <[EMAIL PROTECTED]> wrote: > > Here is one way of doing it: > > > > > x > > [,1] [,2] [,3] > > [1,] 2 4 6 > > [2,] 1 2 NA > > [3,] 4 6 NA > > > y > > [,1] [,2] [,3] > > [1,] NA 4 4 > > [2,] 2 2 NA > > [3,] 1 2 2 > > > z <- mapply(function(a,b)mean(c(a,b), na.rm=TRUE), x, y) > > > dim(z) <- dim(x) > > > z > > [,1] [,2] [,3] > > [1,] 2.0 4 5 > > [2,] 1.5 2 NaN > > [3,] 2.5 4 2 > > > # to change it to NA > > > is.na(z) <- is.nan(z) > > > z > > [,1] [,2] [,3] > > [1,] 2.0 4 5 > > [2,] 1.5 2 NA > > [3,] 2.5 4 2 > > > > > > > > > > > > > > On Nov 11, 2007 4:52 PM, affy snp <[EMAIL PROTECTED]> wrote: > > > Dear list, > > > > > > I am new to R and very inexperienced. Sorry for the trouble. > > > I have two txt files and want to merge them by taking the average. > > > More specifically, for example, the txt file1, with row names and column > > > names, > > > consists of 238000 rows and 196 columns. Each column corresponds > > > to a sample. The data is mixed with numeric or NA. So what I plan to > > > do is: > > > > > > (1) Take the 1st column from txt file 1 and txt file 2, calculate the > > > average > > > if both numbers are numeric. If one is numeric and the other one is NA or > > > the opposite, just use the numeric; If both are NA, then use NA, Do all > > > this > > > for all columns > > > (2) Create txt file 3 with the numbers from the above and add the row > > > names and > > > column names. > > > > > > So an illustrative example could be: > > > > > > txt file 1 > > > > > > A B C > > > row1 2 4 6 > > > row2 1 2 NA > > > row3 4 6 NA > > > > > > txt file 2 > > > > > > A B C > > > row1 NA 4 4 > > > row2 2 2 NA > > > row3 1 2 2 > > > > > > then txt file 3 will be created as: > > > > > > A B C > > > row1 2 4 5 > > > row2 1.5 2 NA > > > row3 2.5 4 2 > > > > > > Any help will be appreciated. > > > > > > Thanks! > > > Allen > > > > > > ______________________________________________ > > > 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. > > > > > > > > > > > -- > > Jim Holtman > > Cincinnati, OH > > +1 513 646 9390 > > > > What is the problem you are trying to solve? > > > -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? ______________________________________________ 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.
