[BioC] [MAANOVA] Warnings in fitmaanova & information request
Loren Engrav
engrav at u.washington.edu
Fri Mar 12 03:07:33 CET 2010
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
> From: Maciej Jończyk <mjonczyk at biol.uw.edu.pl>
> Reply-To: Maciej Jończyk <mjonczyk at biol.uw.edu.pl>
> Date: Thu, 11 Mar 2010 12:11:10 +0100
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Cc: Maciej Jończyk <mjonczyk at biol.uw.edu.pl>
> Subject: [BioC] [MAANOVA] Warnings in fitmaanova & information request
>
> Firstly I want to apologise for my top-posting.
I won't do that in
> future.
Dear list members,
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_d
> hc093 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_dlk0
> 92 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_dhc1
> 21 Cy5 5 dh c 3
dlk_dhc121 Cy3 11 dl k 3
dhc_dlk015 Cy5 12 dl k 4
dhc_dlk015 C
> y3 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).
My data file is organised exactly as
> described in manual.
I've read the
> data:
>eth_logrg=read.madata("./eth4maan",designfile=".des4maanova",
arrayType
> ="twoColor",header=TRUE,spotflag=FALSE,log.trans=TRUE,
metarow=2,metacol=3,row
> =4,col=5,probeid=1,intensity=6)
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.
>model.full_nodye=fitmaanova(eth_logrg,formula=~Array+Sample
>
+powt_b+linia+temp+linia:temp,random=~Array+Sample+powt_b)
After this code I
> get warning messages. Here it is:
...
Finish gene number 42500 ...
Finish
> gene number 42600 ...
Finish gene number 42700 ...
Finish gene number 42800
> ...
Finish gene number 42900 ...
Finish gene number 43000 ...
Finish gene
> number 43100 ...
Finish gene number 43200 ...
Finish gene number 43300
> ...
Warning messages:
1: In any(result$random[idx.mainterm]) :
coercing
> argument of type 'double' to logical
2: In any(parsed.formula$random) :
> coercing argument of type 'double' to logical
3: In
> any(result$random[idx.mainterm]) :
coercing argument of type 'double' to
> logical
4: In any(parsed.formula$random) :
coercing argument of type
> 'double' to logical
What it means? I've got the object I specified, is it
> valid?
> summary(model.full_nodye)
Length Class
> Mode
probeid 43381 -none- character
yhat 2082288
> -none- numeric
S2 173524 -none- numeric
loops
> 43381 -none- numeric
S2.level 3 -none- character
G
> 43381 -none- numeric
Array 1041144 -none- numeric
Array.level
> 24 -none- character
Sample 694096 -none- numeric
Sample.level
> 16 -none- numeric
powt_b 173524 -none- numeric
powt_b.level
> 4 -none- numeric
linia 86762 -none- numeric
linia.level
> 2 -none- character
temp 86762 -none- numeric
temp.level
> 2 -none- character
linia:temp 173524 -none- numeric
linia:temp.level
> 4 -none- character
model 12 mamodel list
subCol
> 1 -none- logical
I also would like to request more information about usage
> of
the MAANOVA package.
I've read manual and material from this list
> and
http://churchill.jax.org/software/rmaanova.shtml.
In particular I'd like
> to find out how to set up contrasts,
like e.g. dhc vs dhk.
Best
> Regards,
Maciej Jończyk
Department of Plant Molecular Ecophysiology
Institute
> of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096
> Warszawa, Miecznikowa 1
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