On Feb 3, 2012, at 6:17 PM, brann...@mskcc.org wrote:
Hello,
I'm trying to replace any value within a column where the value is
less than 10% of the median of the column with NA. In other words,
if the median of one column is 500, any value in that column that is
less than 50 should become NA.
Doing a lot of searches, it seems like I should be using apply. But
when I put the if statement inside like this, I get serious errors:
You didn't show str(gc2) or show us how it might be built.
test<-apply(gc2,2,function(x){if(x<(0.1*median(x))), NA})
Error: unexpected ',' in "test<-apply(gc2,2,function(x)
{if(x<(0.1*median(x))),"
You want ifelse() rather than if(). You also will need to look more
carefully at how 'ifelse' is designed.
test<-apply(gc2,2,function(x){if(x<(0.1*median(x))) NA})
There were 50 or more warnings (use warnings() to see the first 50)
In if (x < (0.1 * median(x))) x <- NA :
the condition has length > 1 and only the first element will be used
Trying
test<-apply(gc2,2,function(x){x[x<(0.1*median(x))]<- NA})
head(test)
NA.01.N NA.01.T NA.02.N NA.02.T NA.03.N NA.03.T
NA NA NA NA NA NA
That probably indicates that you need to look more carefully at ?
median because it appears you have at least one NA in each of your
gc2 columns.
I'm sure that I could get it to work if I read each column
individually into a vector, calculate the median, replace the values
if less than 0.1*median, then rebind it into a new matrix. However,
I'm hoping there is a more elegant way.
Perhaps the sweep function?
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David Winsemius, MD
West Hartford, CT
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