[BioC] R/maanova warnings(): coercing argument of type 'double' to logical

[Thierry Janssens]

Dear BioC,

 while doing the R/maanova fitmaanova() and matest() functions I always 
encounter the following warnings (bold) which make me worry:

 > maanovatest <- fitmaanova(rawdata, formula = ~Dye+Array+Diet, random 
= ~Array)
Calculating variance components for fixed model...
Fitting mixed effect model...
Finish gene number 100 ...
Finish gene number 200 ...
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Finish gene number 5000 ...
*Warning messages:
1: In any(parsed.formula$random) :
  coercing argument of type 'double' to logical
2: In any(parsed.formula$random) :
  coercing argument of type 'double' to logical*
 > test.maanovaDiet <- matest(rawdata, maanovatest, term ="Diet", n.perm 
= 5)
Doing F-test on observed data ...
Doing permutation. This may take a long time ...
There were 15 warnings (use warnings() to see them)
 > warnings()
Warning messages:
*1: In FUN(newX[, i], ...) : coercing argument of type 'double' to logical
2: In FUN(newX[, i], ...) : coercing argument of type 'double' to logical
3: In FUN(newX[, i], ...) : coercing argument of type 'double' to logical
4: In FUN(newX[, i], ...) : coercing argument of type 'double' to logical
5: In FUN(newX[, i], ...) : coercing argument of type 'double' to logical
6: In any(parsed.formula$random) : coercing argument of type 'double' to 
logical
7: In any(parsed.formula$random) : coercing argument of type 'double' to 
logical
8: In any(parsed.formula$random) : coercing argument of type 'double' to 
logical
9: In any(parsed.formula$random) : coercing argument of type 'double' to 
logical
10: In any(parsed.formula$random) : coercing argument of type 'double' 
to logical
11: In any(parsed.formula$random) : coercing argument of type 'double' 
to logical
12: In any(parsed.formula$random) : coercing argument of type 'double' 
to logical
13: In any(parsed.formula$random) : coercing argument of type 'double' 
to logical
14: In any(parsed.formula$random) : coercing argument of type 'double' 
to logical
15: In any(parsed.formula$random) : coercing argument of type 'double' 
to logical
*

My designmatrix is as follows

Array	Dye	Diet	Sample
1	Cy3	4	1
1	Cy5	1	2
2	Cy3	5	3
2	Cy5	4	4
3	Cy3	3	5
3	Cy5	5	6
4	Cy3	2	7
4	Cy5	3	8
5	Cy3	1	9
5	Cy5	2	10
6	Cy3	5	11
6	Cy5	1	12
7	Cy3	2	13
7	Cy5	5	14
8	Cy3	4	15
8	Cy5	2	16
9	Cy3	3	17
9	Cy5	4	18
10	Cy3	1	19
10	Cy5	3	20

and the datafile  consists of

of the following columns

Row	Col	GeneName	Description	SSArray1 Cy3	SSArray1 Cy5	SSArray2 Cy3	SSArray2 Cy5	SSArray3 Cy3	SSArray3 Cy5	SSArray4 Cy3	SSArray4 Cy5	SSArray5 Cy3	SSArray5 Cy5	SSArray6 Cy3	SSArray6 Cy5	SSArray7 Cy3	SSArray7 Cy5	SSArray8 Cy3	SSArray8 Cy5	SSArray9 Cy3	SSArray9 Cy5	SSArray10 Cy3	SSArray10 Cy5		

Are these warnings caused by a bug or is the structure of my dataset causing this?

> sessionInfo()
R version 2.8.1 (2008-12-22) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] maanova_1.13.1 statmod_1.3.8  limma_2.16.4  


Kind regards,

Thierry 
 





-- 
Thierry K.S. Janssens
Vrije Universiteit Amsterdam
Faculty of Earth and Life Sciences
Institute of Ecological Science
Department of Animal Ecology,
De Boelelaan 1085
1081 HV AMSTERDAM, The Netherlands
Phone: +31 (0)20-5989147
Fax: +31 (0)20-5987123
thierry.janssens at ecology.falw.vu.nl