Dear Gordon,
   
  Thank you for your reply. Yes, of course, in my case lmFit just doesn't contain the Amean slot.
  Thank you.
   
  Could you please comment on my previous question, subject LIMMA (there were three messages from me)? I would be really grateful for any suggestions.
   
  With kind regards,
  Lev.

Gordon Smyth <smyth@wehi.EDU.AU> wrote:
  Dear Lev,

You've broken the code by sort of over-programming with

lmFit(log2(exp(exprs(temp))), design)

If you used the simpler

lmFit(temp, design)

it would all work.

The problem is that you're giving lmFit a matrix not an expression 
object, hence lmFit doesn't know whether the data are log-ratios or 
log-intensities, hence it can't compute the Amean values, hence it 
can't make an MA-plot. There's been some discussion about this topic 
on this list.

Best wishes
Gordon

PS. Please give sessionInfo() when you make a post. I'm guessing here 
that you're not using the current Bioconductor release.

At 01:45 AM 10/05/2007, Lev Soinov wrote:
>Dear List,
>
>Could you shed some light on what this mistake might mean:
> > plotMA(fit2, array=1)
>Error in xy.coords(x, y, xlabel, ylabel, log) :
> 'x' and 'y' lengths differ
>In addition: Warning messages:
>1: is.na() applied to non-(list or vector) in: is.na(x)
>2: no non-missing arguments to min; returning Inf
>3: no non-missing arguments to max; returning -Inf
>
>My scripts are below.
>With kind regards,
>Lev.
>
>
>
> > signals[1:2,1:2]
> SIGNAL1 SIGNAL2
>1 761.96 825.94
>2 16059.83 15860.98
> > print (nrow (signals))
>[1] 11691
> > print (ncol (signals))
>[1] 20
> > temp<-vsn(signals)
>vsn: 11691 x 20 matrix (1 stratum). 100% done.
> >
> >
> > design <- model.matrix(~0 
> +factor(c(1,1,1,1,2,1,2,2,2,2,3,3,3,3,4,4,4,4,4,3)))
> > colnames(design) <- c("group1", "group2", "group3", "group4")
> > contrast.matrix <- makeContrasts(group2-group1, group3-group1, 
> group4-group1, group4-group2, group4-group3, group3-group2, levels=design)
> > fit <- lmFit(log2(exp(exprs(temp))), design)
> > fit2 <- contrasts.fit(fit, contrast.matrix)
> > fit2 <- eBayes(fit2)



 		
---------------------------------

	[[alternative HTML version deleted]]

