R help - May 2010 - strange error msg from lapply and lm()

I am conducting a very simple t test for two genes using lapply (i try to
avoid loop since i will have thousands of genes later on). however, I got
strange error msg like the followings. It looks that R is complaining my
factor has only one level, which is not the case (I check many times).
> result<- lapply(split(all,all$CHIPEXP_NAME),function(x)
> lm(logvalue~treatment,x))
Error in `contrasts<-`(`*tmp*`, value = "contr.treatment") : 
  contrasts can be applied only to factors with 2 or more levels


can anyone help me to dissect this problem?

thanks in advance.


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plus, it took long time to complete this analysis for only 24 records!
Although I get the error msg, the result seems to be correct.


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Hi

r-help-bounces at r-project.org napsal dne 03.05.2010 16:24:11:
> 
> I am conducting a very simple t test for two genes using lapply (i try 
to
> avoid loop since i will have thousands of genes later on). however, I 
got
> strange error msg like the followings. It looks that R is complaining my
> factor has only one level, which is not the case (I check many times).
In each split?

sum(rowSums(sapply(split(all$treatment,all$CHIPEXP_NAME), function(x) 
table(x))>0)<2)

shall tell you if there are some parts of your split which has only 1 or 
less non empty levels.

What is the result in your case? Shall be zero.

Regards
Petr

> 
> > result<- lapply(split(all,all$CHIPEXP_NAME),function(x)
> > lm(logvalue~treatment,x))
> Error in `contrasts<-`(`*tmp*`, value = "contr.treatment") : 
>   contrasts can be applied only to factors with 2 or more levels
> 
> 
> can anyone help me to dissect this problem?
> 
> thanks in advance.
> 
> 
> -- 
> View this message in context: 
http://r.789695.n4.nabble.com/strange-error-msg-
> from-lapply-and-lm-tp2124042p2124042.html
> Sent from the R help mailing list archive at Nabble.com.
> 
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