Try this:
apply(gc2, 2, function(x) ifelse(x < 0.1*median(x), NA, x)}
ifelse is the vectorized operation you are probably looking for.
Michael
On Fri, 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:
>
>> 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))),"
>> 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
>
>
> 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.
>
> Do you have any suggestions?
>
>
> Thank you for your help.
> Rose
>
>
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