[BioC] Non-conformable arguments fitting limma contrasts
paul.boutros at utoronto.ca
paul.boutros at utoronto.ca
Tue Jul 27 03:43:10 CEST 2004
Hello,
I've come across an error when fitting contrasts with Affy data using limma.
I'm on:
WinXP SP1
R1.9.1
limma 1.7.2
gcrma 1.1.0
arrays: RAE230A
The error message I'm getting is:
> fit2 <- contrasts.fit(fit1, contrast.matrix);
Error in o %*% RUC^2 : non-conformable arguments
> traceback();
1: contrasts.fit(fit1, contrast.matrix)
Below I've appended the sequence of commands I'm using, followed by my
pData(eset), my design and contrast matrices.
Briefly, what I have are the following factors:
Strain: four levels (HW, LE, LnC, LnA)
Time: two levels (hour3, hour19)
Treatment: two levels (TCDD, COil)
AHR Genotype: two levels (HW, WT)
Where I believe I may have gone wrong is explicitly including the AHR genotype
in the model. This factor can be determined by the strain: two strains (HW,
LnA) always have AHR = HW while the other two strains always have AHR = WT.
Including both surely feels like double-fitting to me. On the other hand, the
AHR genotype is *not* the only factor differing between the strains which was my
motivation for including it.
As always, I'm open to any comments/suggestions/corrections.
Paul
### Start Command Sequence ###
eset <- ReadAffy(filenames=cel.files, phenoData="phenodata.txt");
eset <- gcrma(eset);
# create a design matrix:
design <- model.matrix(~-1 + Strain + Treatment + Time + AHR + AHR:Treatment +
AHR:Time, pData(eset));
colnames(design) <- c("HW", "LE", "LnA", "LnC", "TCDD", "Time", "WT", "WT.TCDD",
"WT.Time");
# make a contrast matrix
contrast.matrix <- makeContrasts(TCDD, Time, -WT, -WT.TCDD, -WT.Time,
levels=design);
# fit the model
fit1 <- lmFit(eset, design);
fit2 <- contrasts.fit(fit1, contrast.matrix);
fit3 <- eBayes(fit2);
### End Command Sequence ###
> pData(eset);
Strain Treatment Time AHR
RAE230A_021304_IM01T_LH.CEL HW TCDD Hour3 HW
RAE230A_021304_IM02T_LH.CEL HW TCDD Hour3 HW
RAE230A_021304_IM03T_LH.CEL HW TCDD Hour3 HW
RAE230A_021304_IM04T_LH.CEL HW TCDD Hour3 HW
RAE230A_021304_IM05T_LH.CEL LE TCDD Hour3 WT
RAE230A_021304_IM06T_LH.CEL LE TCDD Hour3 WT
RAE230A_021304_IM07T_LH.CEL LE TCDD Hour3 WT
RAE230A_021304_IM08T_LH.CEL LE TCDD Hour3 WT
RAE230A_043003_IM01T_LH.CEL LE TCDD Hour19 WT
RAE230A_043003_IM02T_LH.CEL LE COil Hour19 WT
RAE230A_043003_IM03T_LH.CEL HW COil Hour19 HW
RAE230A_043003_IM04T_LH.CEL HW TCDD Hour19 HW
RAE230A_060403_IM01T_LH.CEL LE COil Hour19 WT
RAE230A_060403_IM02T_LH.CEL LE COil Hour19 WT
RAE230A_060403_IM03T_LH.CEL LE COil Hour19 WT
RAE230A_060403_IM04T_LH.CEL HW COil Hour19 HW
RAE230A_060403_IM05T_LH.CEL HW COil Hour19 HW
RAE230A_060403_IM06T_LH.CEL LE TCDD Hour19 WT
RAE230A_060403_IM07T_LH.CEL LE TCDD Hour19 WT
RAE230A_060403_IM08T_LH.CEL LE TCDD Hour19 WT
RAE230A_060403_IM09T_LH.CEL HW TCDD Hour19 HW
RAE230A_060403_IM10T_LH.CEL HW TCDD Hour19 HW
RAE230A_070303_IM01T_LH.CEL HW TCDD Hour19 HW
RAE230A_070303_IM02T_LH.CEL HW COil Hour19 HW
RAE230A_102803_IM01T_LH.CEL LnA COil Hour19 HW
RAE230A_102803_IM02T_LH.CEL LnA COil Hour19 HW
RAE230A_102803_IM03T_LH.CEL LnA COil Hour19 HW
RAE230A_102803_IM04T_LH.CEL LnA COil Hour19 HW
RAE230A_102803_IM05T_LH.CEL LnA TCDD Hour19 HW
RAE230A_102803_IM06T_LH.CEL LnA TCDD Hour19 HW
RAE230A_102803_IM07T_LH.CEL LnA TCDD Hour19 HW
RAE230A_102803_IM08T_LH.CEL LnC COil Hour19 WT
RAE230A_102803_IM09T_LH.CEL LnC COil Hour19 WT
RAE230A_102803_IM10T_LH.CEL LnC COil Hour19 WT
RAE230A_102803_IM11T_LH.CEL LnC COil Hour19 WT
RAE230A_102803_IM12T_LH.CEL LnC TCDD Hour19 WT
RAE230A_102803_IM13T_LH.CEL LnC TCDD Hour19 WT
RAE230A_102803_IM14T_LH.CEL LnC TCDD Hour19 WT
RAE230A_102803_IM15T_LH.CEL LnC TCDD Hour19 WT
RAE230A_102803_IM16T_LH.CEL LnA TCDD Hour19 HW
> design;
HW LE LnA LnC TCDD Time WT WT.TCDD WT.Time
RAE230A_021304_IM01T_LH.CEL 1 0 0 0 1 1 0 0 0
RAE230A_021304_IM02T_LH.CEL 1 0 0 0 1 1 0 0 0
RAE230A_021304_IM03T_LH.CEL 1 0 0 0 1 1 0 0 0
RAE230A_021304_IM04T_LH.CEL 1 0 0 0 1 1 0 0 0
RAE230A_021304_IM05T_LH.CEL 0 1 0 0 1 1 1 1 1
RAE230A_021304_IM06T_LH.CEL 0 1 0 0 1 1 1 1 1
RAE230A_021304_IM07T_LH.CEL 0 1 0 0 1 1 1 1 1
RAE230A_021304_IM08T_LH.CEL 0 1 0 0 1 1 1 1 1
RAE230A_043003_IM01T_LH.CEL 0 1 0 0 1 0 1 1 0
RAE230A_043003_IM02T_LH.CEL 0 1 0 0 0 0 1 0 0
RAE230A_043003_IM03T_LH.CEL 1 0 0 0 0 0 0 0 0
RAE230A_043003_IM04T_LH.CEL 1 0 0 0 1 0 0 0 0
RAE230A_060403_IM01T_LH.CEL 0 1 0 0 0 0 1 0 0
RAE230A_060403_IM02T_LH.CEL 0 1 0 0 0 0 1 0 0
RAE230A_060403_IM03T_LH.CEL 0 1 0 0 0 0 1 0 0
RAE230A_060403_IM04T_LH.CEL 1 0 0 0 0 0 0 0 0
RAE230A_060403_IM05T_LH.CEL 1 0 0 0 0 0 0 0 0
RAE230A_060403_IM06T_LH.CEL 0 1 0 0 1 0 1 1 0
RAE230A_060403_IM07T_LH.CEL 0 1 0 0 1 0 1 1 0
RAE230A_060403_IM08T_LH.CEL 0 1 0 0 1 0 1 1 0
RAE230A_060403_IM09T_LH.CEL 1 0 0 0 1 0 0 0 0
RAE230A_060403_IM10T_LH.CEL 1 0 0 0 1 0 0 0 0
RAE230A_070303_IM01T_LH.CEL 1 0 0 0 1 0 0 0 0
RAE230A_070303_IM02T_LH.CEL 1 0 0 0 0 0 0 0 0
RAE230A_102803_IM01T_LH.CEL 0 0 1 0 0 0 0 0 0
RAE230A_102803_IM02T_LH.CEL 0 0 1 0 0 0 0 0 0
RAE230A_102803_IM03T_LH.CEL 0 0 1 0 0 0 0 0 0
RAE230A_102803_IM04T_LH.CEL 0 0 1 0 0 0 0 0 0
RAE230A_102803_IM05T_LH.CEL 0 0 1 0 1 0 0 0 0
RAE230A_102803_IM06T_LH.CEL 0 0 1 0 1 0 0 0 0
RAE230A_102803_IM07T_LH.CEL 0 0 1 0 1 0 0 0 0
RAE230A_102803_IM08T_LH.CEL 0 0 0 1 0 0 1 0 0
RAE230A_102803_IM09T_LH.CEL 0 0 0 1 0 0 1 0 0
RAE230A_102803_IM10T_LH.CEL 0 0 0 1 0 0 1 0 0
RAE230A_102803_IM11T_LH.CEL 0 0 0 1 0 0 1 0 0
RAE230A_102803_IM12T_LH.CEL 0 0 0 1 1 0 1 1 0
RAE230A_102803_IM13T_LH.CEL 0 0 0 1 1 0 1 1 0
RAE230A_102803_IM14T_LH.CEL 0 0 0 1 1 0 1 1 0
RAE230A_102803_IM15T_LH.CEL 0 0 0 1 1 0 1 1 0
RAE230A_102803_IM16T_LH.CEL 0 0 1 0 1 0 0 0 0
attr(,"assign")
[1] 1 1 1 1 2 3 4 5 6
attr(,"contrasts")
attr(,"contrasts")$Strain
[1] "contr.treatment"
attr(,"contrasts")$Treatment
[1] "contr.treatment"
attr(,"contrasts")$Time
[1] "contr.treatment"
attr(,"contrasts")$AHR
[1] "contr.treatment"
> contrast.matrix;
TCDD Time -WT -WT.TCDD -WT.Time
HW 0 0 0 0 0
LE 0 0 0 0 0
LnA 0 0 0 0 0
LnC 0 0 0 0 0
TCDD 1 0 0 0 0
Time 0 1 0 0 0
WT 0 0 -1 0 0
WT.TCDD 0 0 0 -1 0
WT.Time 0 0 0 0 -1
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