Not reproducible, ball in your court. However, in the meantime, my suggestion 
is to not do that. Convert to character before you alter the factor, then 
convert back when you are done.
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Sent from my phone. Please excuse my brevity.

On September 27, 2014 9:49:41 PM PDT, Kate Ignatius <kate.ignat...@gmail.com> 
wrote:
>Quick question:
>
>I am running the following code on some variables that are factors:
>
>dbpmn$IID1new <- ifelse(as.character(dbpmn[,2]) ==
>as.character(dbpmn[,(21)]), dbpmn[,20], '')
>
>Instead of returning some value it gives me this:
>
>c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1))
>
>Playing around with the code, gives me some kind of variation to it.
>Is there some way to get me what I want.  The variable that its
>suppose to give back is a bunch of sampleIDs.
>
>Thanks!
>
>______________________________________________
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>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

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