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@guest-user-4897
Last seen 10.3 years ago
Dear edgeR maintainers,
I have some troubles setting up the correct design for my DE
experiment. I now how my experiment design should look like and that
is like this:
> design
subject1 subject2 subject3 subject4
S7309 1 0 0 0
S7310 1 0 0 0
S7311 0 1 0 0
S7312 0 1 0 0
S7313 0 0 1 0
S7314 0 0 1 0
S7315 0 0 0 1
S7316 0 0 0 1
attr(,"assign")
[1] 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$subject
[1] "contr.treatment"
After that i make my contrasts:
> makeContrasts(subject1,subject2,subject3,subject4, levels = design)
Contrasts
Levels subject1 subject2 subject3 subject4
subject1 1 0 0 0
subject2 0 1 0 0
subject3 0 0 1 0
subject4 0 0 0 1
This all looks right since i need to compare the subjects with each
other. But when i run my analysis function which looks like this:
library( edgeR );
library( ggplot2 );
library( reshape );
library( FactoMineR );
analyse <- function( counts, design, contrast, name, style ) {
counts <- counts[ rowSums( counts, na.rm = TRUE ) > 0, ];
y <- DGEList( counts = counts, genes = rownames( counts ) );
y <- calcNormFactors( y );
y <- estimateGLMCommonDisp( y, design );
y <- estimateGLMTrendedDisp( y, design, df = 5 );
y <- estimateGLMTagwiseDisp( y, design );
fit <- glmFit( y, design );
lrt <- glmLRT( fit, contrast = contrast );
de <- decideTestsDGE( lrt, p = 0.05, adjust = "BH" );
cpmY <- cpm( y );
daf <- designAsFactor( design );
orderedDesign <- design[ order( daf, names( daf ) ), ];
tab <- data.frame(
row.names = rownames( cpmY ),
genes = rownames( cpmY ),
de = de,
cpmY[ ,order( daf, names( daf ) ) ]
);
aRepTab <- topTags( lrt, n = nrow( counts ) )$table;
aRepTab$rank <- 1:nrow( counts );
# repTab <- tab[ match( aRepTab$genes, rownames( tab ) ), ];
repTab <- merge( aRepTab, tab, by = "genes", sort = FALSE );
repTab <- repTab[ order( repTab$rank ), ];
# data.frame(
# row.names = rownames( aRepTab ),
# aRepTab,
# tab[ match( aRepTab$genes, tab$genes ), ]
# )
list(
name = name,
y = y,
fit = fit,
lrt = lrt,
de = de,
tab = tab,
style = style,
repTab = repTab,
orderedDesign = orderedDesign
);
}
I got the following error:
Error in mglmLevenberg(y, design = design, dispersion = dispersion,
offset = offset, :
BLAS/LAPACK routine 'DGEMM ' gave error code -13
5 mglmLevenberg(y, design = design, dispersion = dispersion, offset =
offset,
weights = weights, coef.start = start, maxit = 250)
4 glmFit.default(glmfit$counts, design = design0, offset =
glmfit$offset,
weights = glmfit$weights, dispersion = glmfit$dispersion,
prior.count = 0)
3 glmFit(glmfit$counts, design = design0, offset = glmfit$offset,
weights = glmfit$weights, dispersion = glmfit$dispersion,
prior.count = 0)
2 glmLRT(fit, contrast = contrast) at diffexpr.R#15
1 analyse(counts, design, contrast, countsId, style)
I tried to use different models but i cannot succeed to avoid the
error for this comparison. (other comparisons do succeed) Any hints
will be very appreciated.
Thanks in advance!
Best regards,
Sander
-- output of sessionInfo():
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics grDevices utils datasets
methods base
other attached packages:
[1] FactoMineR_1.26 reshape_0.8.5 ggplot2_1.0.0 reshape2_1.4
edgeR_3.6.7 limma_3.20.8
loaded via a namespace (and not attached):
[1] car_2.0-20 cluster_1.15.2 colorspace_1.2-4
digest_0.6.4 grid_3.1.0 gtable_0.1.2
[7] htmltools_0.2.4 lattice_0.20-29 leaps_2.9
MASS_7.3-33 munsell_0.4.2 nnet_7.3-8
[13] plyr_1.8.1 proto_0.3-10 Rcpp_0.11.2
rmarkdown_0.2.49 scales_0.2.4 scatterplot3d_0.3-35
[19] stringr_0.6.2 tools_3.1.0 yaml_2.1.13
--
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