[BioC] limma question

[Sean Davis]

On 2/24/06 12:43 PM, "Sun, Yezhou" <yezhou.sun at mssm.edu> wrote:

> 
> Hi, Jim,
> 
> I tried what you suggested but it's still not working. Got same error
> message:
> 
>> fit<-lmFit(d[, -1], design)
> Error in qr(x) : NA/NaN/Inf in foreign function call (arg 1)
> In addition: Warning message:
> NAs introduced by coercion
>> 
> 
> I think the problem is still in data frame but I don't know what it is.
> The user guide has no detailed description for single channel data set.

Actually, I think there are several sections in the limma user guide devoted
to single-channel data analysis.

Do the following:

d1 <- as.matrix(d[,-1])
summary(d1)

This will show you the number of NA's in each column.  Of course, you will
need to determine why those are there, but it can help pin down what is
going on.  

Sean