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 Aur?lie

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. Thanks Aur?lie 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 > > > Aur?lie 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 >> >> Aur?lie >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > > > -- Aur?lie Laugraud PRABI - LBBE B?t. G.Mendel- 1er ?tage 16, rue Rapha?l Dubois 69622 Villeurbanne Cedex