[BioC] limma(B) and maanova(La.svd) questions

Aurélie Laugraud laugraud at biomserv.univ-lyon1.fr
Thu Oct 20 15:54:08 CEST 2005

Dear all,
I can only agree with you on the quality of the data (it was a 2 arrays 
dye swap test so that's why there is no replicate), it could be a very 
likely explanation.
I can manage to figure out this problem linked with LIMMA.
However I can't understand the link with what I have seen in maanova and 
the problem I met.
I would still be very interested in knowing if people have had the same 
kind of things.


Morten Mattingsdal wrote:
> hi...
> Basically you have a weak experiment with too few gene observations 
> (only 2 arrays if I understood you right).
> With so few observations you expect to get rather poor statistics.
> I would expand your experiment (dont dye-swap:) with more biological 
> replicates if  I were you.
> mvh
> morten
> Aurélie Laugraud wrote:
>> Hello,
>> I am working on 2-color arrays, 2 arrays (2 conditions), 27648 spots. 
>> my first try with maanova was very unsuccessful as
>> there was an problem with the degrees of freedom ( model contained 
>> Array+Dye+Sample ...I don't think it is too much but it was). My 
>> second try was to put Array as random but I got this:
>> "Fitting mixed effect model...
>> Erreur dans La.svd(X, method = "dgesvd") : infinite or missing values 
>> in 'x'"
>> I have no idea what to change to make it happy, I however found out 
>> that it is very likely the function "pinv" in "mixed" that is unhappy...
>> Then I tried limma, everything went find and ok until I had a look at 
>> the "B" value which was terrifyingly low (the best I can get is 0.67 
>> for the best score). I tried quite a lot of different values for the 
>> parameters but it doesn't seem to
>> change the real underlying problem there.
>> Does anyone haven any idea or have seen the same things ?
>> Thanks
>> Aurélie
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Aurélie Laugraud
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16, rue Raphaël Dubois
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