[BioC] [MAANOVA] Warnings in fitmaanova & information request
Maciej Jończyk
mjonczyk at biol.uw.edu.pl
Sat Mar 13 17:54:39 CET 2010
Thank you Loren, I'll ignore this error.
>From: Loren Engrav <engrav <at> u.washington.edu>
>Subject: Re: [MAANOVA] Warnings in fitmaanova & information request
>Newsgroups: gmane.science.biology.informatics.conductor
>Date: 2010-03-12 02:07:33 GMT (1 day, 14 hours and 34 minutes ago)
>
>Greetings
>
>If you are asking is this warning significant
>
>> Warning messages:
>1: In any(result$random[idx.mainterm]) :
> coercing
>> argument of type 'double' to logical
>2
>
>I have used maanova many many times and see that message every time and
the
>maanova people indicated I should ignore it
But I have next problem and I want to ask for advice.
*
I pasted some of the previous supplied information (I can't respond from
list level,
I respond to verification message but it was a day ago and nothing
happens :( ).
#####################################################################
I'm trying to analyse simple loop-design in MAANOVA package.
I've used two-colour spotted oligo arrays.
I have two maize lines (linia): dl, dh;
two conditions (temp): c (cold), k (control).
Here is my design:
dlc ---- dlk
| X |
dhc ---- dhk
with two more hybridizations, dlc vs dhk and dlk vs dhc ("X" in this
scheme).
I repeated this scheme four times, with dye swap (two labelings in
both directions).
Technical replication is within each replicated scheme. So within
scheme all instances of each sample (samples: dlc, dlk, dhc, dhk)
is from the same isolation (i.e. in each loop each RNA is used
three times in different hybridizations).
Here is my design file (powt_b is a number of biological replicate):
Array Dye Sample linia temp powt_b
dhk_dhc093 Cy5 1 dh c 1
dhk_dhc093 Cy3 2 dh k 1
dhc_dhk104 Cy5 3 dh k 2
dhc_dhk104 Cy3 4 dh c 2
dhk_dhc116 Cy5 5 dh c 3
dhk_dhc116 Cy3 6 dh k 3
dhc_dhk016 Cy5 7 dh k 4
dhc_dhk016 Cy3 8 dh c 4
dhk_dlk094 Cy5 9 dl k 1
dhk_dlk094 Cy3 2 dh k 1
dlk_dhk105 Cy5 3 dh k 2
dlk_dhk105 Cy3 10 dl k 2
dhk_dlk117 Cy5 11 dl k 3
dhk_dlk117 Cy3 6 dh k 3
dlk_dhk139 Cy5 7 dh k 4
dlk_dhk139 Cy3 12 dl k 4
dlc_dlk092 Cy5 9 dl k 1
dlc_dlk092 Cy3 13 dl c 1
dlk_dlc106 Cy5 14 dl c 2
dlk_dlc106 Cy3 10 dl k 2
dlc_dlk118 Cy5 11 dl k 3
dlc_dlk118 Cy3 15 dl c 3
dlk_dlc023 Cy5 16 dl c 4
dlk_dlc023 Cy3 12 dl k 4
dlc_dhc095 Cy5 1 dh c 1
dlc_dhc095 Cy3 13 dl c 1
dhc_dlc107 Cy5 14 dl c 2
dhc_dlc107 Cy3 4 dh c 2
dlc_dhc119 Cy5 5 dh c 3
dlc_dhc119 Cy3 15 dl c 3
dhc_dlc136 Cy5 16 dl c 4
dhc_dlc136 Cy3 8 dh c 4
dlk_dhc101 Cy5 1 dh c 1
dlk_dhc101 Cy3 9 dl k 1
dhc_dlk103 Cy5 10 dl k 2
dhc_dlk103 Cy3 4 dh c 2
dlk_dhc121 Cy5 5 dh c 3
dlk_dhc121 Cy3 11 dl k 3
dhc_dlk015 Cy5 12 dl k 4
dhc_dlk015 Cy3 8 dh c 4
dhk_dlc100 Cy5 13 dl c 1
dhk_dlc100 Cy3 2 dh k 1
dlc_dhk102 Cy5 3 dh k 2
dlc_dhk102 Cy3 14 dl c 2
dhk_dlc120 Cy5 15 dl c 3
dhk_dlc120 Cy3 6 dh k 3
dlc_dhk140 Cy5 7 dh k 4
dlc_dhk140 Cy3 16 dl c 4
As required, Sample denotes distinct RNAs. So, e.g. condition
"dl c" has the same number within single replication of entire
scheme (what makes three technical replicates of RNA withnin
biological replicate).
I wrote the model. I want to include factors linia, powt and
their interaction as a fixed effects. I also included Sample,
powt_b and Array as a random effects. In this way I want to
include effect of techical replication. I didn't include Dye
effect, because the experiment was dye balanced, and data
normalized.
######################################################################
After "fitmaanova":
>model.full_nodye=fitmaanova(eth_logrg,formula=~Array+Sample+powt_b+linia+temp
+linia:temp,random=~Array+Sample+powt_b)
I wanted to set up contrasts for interaction terms:
dlc vs dlk
dhc vs dhk
dlc vs dhc
dlk vs dhk
I constructed design matrix (I suppose that variants are ordered
alphabetically).
>cont_matx=matrix(c(1,-1,0,0,0,0,1,-1,1,0,-1,0,0,1,0,-1),nrow=4,byrow=T)
And I tried to perform test
>test=matest(eth_logrg,model.full_nodye,term="linia:temp",Contrast=cont_matx,
n.perm=61,shuffle.method="resid")
But it gave error message:
Error: The number 1 test is not estimable
What is wrong? Am I included too many effects in fitmaanova?
I have four replications of the experiment, I think it is enought.
Or maybe my contrasts' specification is wrong?
I haven't a clue what is wrong.
Help will be very appreciated.
Best wishes,
Maciej
Maciej Jończyk PhD
Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa 1
___________________________________
NOCC, http://nocc.sourceforge.net
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