[BioC] LIMMA: warning coercing argument of type 'double' to logical
Gordon K Smyth
smyth at wehi.EDU.AU
Thu May 28 00:47:05 CEST 2009
Dear Guido,
The warning is not a problem, it does not affect your results. However I
will fix the code so the warning does not occur in this situation.
Best wishes
Gordon
> Date: Tue, 26 May 2009 23:23:10 +0200
> From: "Hooiveld, Guido" <Guido.Hooiveld at wur.nl>
> Subject: [BioC] LIMMA: warning coercing argument of type 'double' to
> logical
> To: <bioconductor at stat.math.ethz.ch>
>
>
> I am learning myselves to run a paired t-test in limma. Everything goes
> fine, but i do encounter a warning, which for me is very vague...
>
>> fit2 <- contrasts.fit(fit, cont.matrix)
> Warning message:
> In any(contrasts[-est, ]) : coercing argument of type 'double' to
> logical
>
> (find the complete code is used below; warning happens at almost the
> end)
>
> I do know that warnings are not equal to errors, but still i would like
> to know what this warning means, and if possible how to avoid it.
>
> Thanks,
> Guido
>
>
>
>
>
>> library(affy)
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>
>> library(limma)
>> targets <- readTargets("targets_A23_paired.txt")
>> targets
> FileName SibShip Strain Treatment
> 1 KOcontrol2.CEL 1 KO Con
> 2 KOcontrol3.CEL 2 KO Con
> 3 KOcontrol5.CEL 3 KO Con
> 4 KOWY7.CEL 1 KO WY
> 5 KOWY8.CEL 2 KO WY
> 6 KOWY9.CEL 3 KO WY
> 7 WTcontrol20.CEL 4 WT Con
> 8 WTcontrol21.CEL 5 WT Con
> 9 WTcontrol22.CEL 6 WT Con
> 10 WTWY25.CEL 4 WT WY
> 11 WTWY26.CEL 5 WT WY
> 12 WTWY27.CEL 6 WT WY
>
>
>> data <- ReadAffy(filenames=targets$FileName)
>> eset <- rma(data)
> Background correcting
> Normalizing
> Calculating Expression
>> eset
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 22690 features, 12 samples
> element names: exprs
> phenoData
> sampleNames: KOcontrol2.CEL, KOcontrol3.CEL, ..., WTWY27.CEL (12
> total)
> varLabels and varMetadata description:
> sample: arbitrary numbering
> featureData
> featureNames: 1415670_at, 1415671_at, ..., AFFX-TrpnX-M_at (22690
> total)
> fvarLabels and fvarMetadata description: none
> experimentData: use 'experimentData(object)'
> Annotation: moe430a
>
>
>> TS <- paste(targets$Strain, targets$Treatment, sep=".")
>> TS
> [1] "KO.Con" "KO.Con" "KO.Con" "KO.WY" "KO.WY" "KO.WY" "WT.Con"
> "WT.Con" "WT.Con" "WT.WY" "WT.WY" "WT.WY"
>> TS <- factor(TS, levels=c("WT.Con","WT.WY","KO.Con","KO.WY"))
>> SibShip <- factor(targets$SibShip)
>> TS
> [1] KO.Con KO.Con KO.Con KO.WY KO.WY KO.WY WT.Con WT.Con WT.Con
> WT.WY WT.WY WT.WY
> Levels: WT.Con WT.WY KO.Con KO.WY
>> SibShip
> [1] 1 2 3 1 2 3 4 5 6 4 5 6
> Levels: 1 2 3 4 5 6
>> design <- model.matrix(~0+TS+SibShip)
>> design
> TSWT.Con TSWT.WY TSKO.Con TSKO.WY SibShip2 SibShip3 SibShip4 SibShip5
> SibShip6
> 1 0 0 1 0 0 0 0 0
> 0
> 2 0 0 1 0 1 0 0 0
> 0
> 3 0 0 1 0 0 1 0 0
> 0
> 4 0 0 0 1 0 0 0 0
> 0
> 5 0 0 0 1 1 0 0 0
> 0
> 6 0 0 0 1 0 1 0 0
> 0
> 7 1 0 0 0 0 0 1 0
> 0
> 8 1 0 0 0 0 0 0 1
> 0
> 9 1 0 0 0 0 0 0 0
> 1
> 10 0 1 0 0 0 0 1 0
> 0
> 11 0 1 0 0 0 0 0 1
> 0
> 12 0 1 0 0 0 0 0 0
> 1
> attr(,"assign")
> [1] 1 1 1 1 2 2 2 2 2
> attr(,"contrasts")
> attr(,"contrasts")$TS
> [1] "contr.treatment"
>
> attr(,"contrasts")$SibShip
> [1] "contr.treatment"
>
>> fit <- lmFit(eset, design)
> Coefficients not estimable: SibShip6
> Warning message:
> Partial NA coefficients for 22690 probe(s)
>
>> cont.matrix <- makeContrasts(WTwyvWTc=TSWT.WY-TSWT.Con,
> KOwyvKOc=TSKO.WY-TSKO.Con, Diff=(TSWT.WY-TSWT.Con)-(TSKO.WY-TSKO.Con),
> levels=design)
>> fit2 <- contrasts.fit(fit, cont.matrix)
> Warning message:
> In any(contrasts[-est, ]) : coercing argument of type 'double' to
> logical
>
>> fit2 <- eBayes(fit2)
>> topTable(fit2, coef=1, adjust="BH")
> ID logFC AveExpr t P.Value adj.P.Val
> B
> 17177 1449065_at 4.528581 6.713129 66.51179 3.781733e-16 8.580752e-12
> 24.96342
> 7192 1422997_s_at 4.298410 8.311977 56.45944 2.444477e-15 2.773259e-11
> 23.90403
> 16494 1448382_at 3.386068 9.658716 50.20860 9.290666e-15 6.124439e-11
> 23.04600
> 13289 1431833_a_at 3.538370 7.856618 49.48486 1.095883e-14 6.124439e-11
> 22.93425
> 7120 1422925_s_at 3.149781 8.072523 48.58693 1.349590e-14 6.124439e-11
> 22.79159
> 18706 1450643_s_at 2.847376 7.907519 44.87659 3.329207e-14 1.258995e-10
> 22.15116
> 296 1415965_at 3.749143 5.293939 43.70413 4.497336e-14 1.457779e-10
> 21.93016
> 12200 1428005_at 3.232843 6.882881 42.99986 5.408650e-14 1.534028e-10
> 21.79272
> 9048 1424853_s_at 4.716858 8.082727 40.20307 1.160545e-13 2.845272e-10
> 21.20948
> 6721 1422526_at 2.772829 8.060643 39.92966 1.253976e-13 2.845272e-10
> 21.14905
>>
>
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> 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] moe430acdf_2.4.0 limma_2.18.0 affy_1.22.0 Biobase_2.4.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.12.0 preprocessCore_1.6.0 tools_2.9.0
>
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> internet: http://nutrigene.4t.com <http://nutrigene.4t.com/>
> email: guido.hooiveld at wur.nl
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