2007/8/2, Gordon K Smyth <smyth@wehi.edu.au>:
>
> > Date: Mon, 30 Jul 2007 12:39:19 +0200
> > From: "Francesco Favero" <favero.francesco@gmail.com>
> > Subject: [BioC] One-Color Agilent miRNA microarrays
>
> ...
> > fit <- lmFit(MA,design,ndups=20,spacing=1,correlation=dupcor$consensus)
> >> Errore in chol(V) : il minore principale di ordine 2 non è definito
> >> positivo
> >
> > (Sorry for the error in Italian...anyway...)
> > It works if I don't use ndups, but I need this...
>
> What sort of object is MA?  Is it just a matrix, or is it a MAList?


It's just a list of log2 intensities even if is the output of
normalizeBetweenArrays function.

What version of limma?


I'm using limma 2.10.5 with R 2.5.1 and BioConductor version 2.0

In any data analysis, you should check you results at every step.  For
> example, have you looked at
> your normalized data?  What is the value of corfit$consensus?


Yes,  I have  a corfit$consensus of 1. I've seen it's for this I can't use
lmFit.
I use ndups=20 so I expect to have some differences between different spot
for the same genes.. in fact atanh.correlations is good for some gene, but
for a lot is Inf or NA, maybe this is because only few spots have a good
Intensity, in average the intensity is very low. this is a problem for miRNA
in cell-lines. Anyway I think it' possible I still have to work on
RG$weigths.

Is it so wrong go around all those problems using lm.series function?

Best wishes
> Gordon


Thanks a lot.

Best Regards,

Francesco
-- 
Cancer Genomics Lab.
"Edo e Elvo Tempia" Foundation.
Via Malta 3 13900 Biella
Tel +39 015351830
http://www.fondoedotempia.it/sub_lab.php

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