Try this; what you want to do is to change the 'levels' of the factor.
> x <- factor(c(1:10,'x','y','xy'))
> str(x)
Factor w/ 13 levels "1","10","2","3",..: 1 3 4 5 6 7 8 9 10 2 ...
> x
[1] 1 2 3 4 5 6 7 8 9 10 x y xy
Levels: 1 10 2 3 4 5 6 7 8 9 x xy y
> # your error
> x[x == 'x'] <- 23
Warning message:
In `[<-.factor`(`*tmp*`, x == "x", value = 23) :
invalid factor level, NAs generated
> x
[1] 1 2 3 4 5 6 7 8 9 10 <NA> y xy
Levels: 1 10 2 3 4 5 6 7 8 9 x xy y
>
> # work with the levels which is what you want to change
> x <- factor(c(1:10,'x','y','xy'))
> levels(x)[x == 'x'] <- '23'
> x
[1] 1 2 3 4 5 6 7 8 9 10 23 y xy
Levels: 1 10 2 3 4 5 6 7 8 9 23 xy y
>
On Wed, Jul 9, 2008 at 5:13 AM, Booman, M <[EMAIL PROTECTED]> wrote:
> Dear all,
>
> Probably a very basic question but I need some help.
> I have a data frame (made by read.table from a text file) of microarray data,
> of which the first column is a factor and the rest of the columns are numeric.
> The factor column contains chromosome names, so values 1 through 22 plus X, Y
> and XY. The numeric columns contain positions or intensity measurements.
> What I need to do is change the X's in the first column to a value of 23.
>
> This is what I thought I would do:
>
> BAF_temp <- read.table("BAF_all.txt", sep="\t", header=T) #to read in the
> table
> BAF_temp[,1][BAF_temp[,1]=="X"] <- 23 #"in rows
> where the first column of BAF_temp is X, change the first column of BAF_temp
> to 23"
>
> However with this last line I get an error: "Invalid factor level, NAs
> generated in '[<-.factor'('*tmp*', BAF_temp[,1]=="X", value=23)"
>
> (I tested if my syntax for selecting the rows of chromosome X was correct by
> trying
> BAF_X <- BAF_temp[BAF_temp[,1]=="X",]
> which worked to give me a data frame with only the rows of the X chromosome.)
>
> I then thought it might work better if I changed the data frame to a matrix.
> When I change the BAF_temp data frame into a matrix (by BAF_matrix <-
> as.matrix(BAF_temp)), then the command I used above:
> BAF_temp[,1][BAF_temp[,1]=="X"] <- 23
> works fine and the end result is as I meant it to be, with all the X's
> changed into 23's.
> However, by using as.matrix all columns are changed to 'character' including
> the numeric measurements (I understand this is because one of the columns of
> the data frame is 'factor')
>
> I would like some help on what is the best option to solve this. I have
> thought of a few options myself and would like your comment/help:
> 1. Is there another syntax I can use on the data frame to change the X's to
> 23's, so I don't have to change the data frame into a matrix first?
>
> 2. I could change the data frame into a matrix and run the syntax as I
> described, resulting in all columns becoming 'character'; is there then an
> easy way to turn the columns with measurements (columns 2 and further) back
> into 'numeric' while leaving the first column with the chromosome numbers as
> 'character'?
>
> 3. I thought of using data.matrix(BAF_temp) and making use of the fact that
> the first column of factors would be changed to the underlying numbers
> (because X being the 23rd level in the list would automaticly be changed to
> 23). However because the levels (chromosome names) of the factor column are
> ordered as "1", "10", "11", "12",....,"19", "2", "20", "21", "3", "4", etc.
> (I see this when using str(BAF_temp)) , this results in chromosome 10 being
> changed into a value of 2, chromosome 11 into 3, chromosome 2 into 12 etc.
> For info: the chromosome names in the text file that is imported are ordered
> just 1, 2, 3, etc.
>
> If anyone has some tips for me I would greatly appreciate it.
>
> Best wishes,
> Marije
>
>
>
>
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--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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