Dear People,
i was trying to implement limma for statistical comparison of a microarray dataset, regarding specific comparisons. Part of my code is the following:
# Other code above skipped for simplicity.. condition <- factor(eset.filtered$Disease, levels=c("Normal","Cancer")) pairs <- factor(rep(1:30, each = 2)) metastatic <- factor(eset.filtered$Meta_factor) f <- paste(condition, metastatic, sep=".") f <- factor(f) design1 <- model.matrix(~0 +f) colnames(design1) <- levels(f) aw <- arrayWeights(eset.filtered, design1) w <- asMatrixWeights(aw, dim(eset.filtered)) dupcor <- duplicateCorrelation(eset.filtered, design1, block=pairs, weights=w) fit <- lmFit(eset.filtered, design1, block=pairs, correlation=dupcor$consensus, weights=w) cm <- makeContrasts(Meta_CancervsMeta_Control="Cancer.1-Normal.1" , levels=design1) fit2 <- contrasts.fit(fit, cm) fit3 <- eBayes(fit2, trend=TRUE)
But then when im calling the function:
top2 <- topTable(fit3, coef="Meta_CancervsMeta_Control", number=nrow(fit3), adjust.method="fdr", sort.by="none")
The following weird error appeared:
Error in .local(fit, n, ...) : unused argument (number = 9065)
Also, when i tried ?topTable i got the two following results:
S4 Generic for obtaining a top table
(in package a4Core in library C:/Program Files/R/R-3.2.2/library)
Table of Top Genes from Linear Model Fit
(in package limma in library C:/Program Files/R/R-3.2.2/library)
Thus, it seems very "naively" that when i run topTable, it utilizes the S4 generic function for topTable from the package a4Core. However, i need this package upstream, in order to use just a function of merging 2 datasets. So, is it possible to explicitly call topTable from limma with a function, in order to avoid the error ? Or as a last alternative, to isolate the merging function from the a4Core package, and create manually this one, in order not to load the package before limma ?
Any help would be greatful !!
*My sessionInfo:
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)
locale:
[1] LC_COLLATE=Greek_Greece.1253 LC_CTYPE=Greek_Greece.1253
[3] LC_MONETARY=Greek_Greece.1253 LC_NUMERIC=C
[5] LC_TIME=Greek_Greece.1253
attached base packages:
[1] stats4 grid parallel stats graphics grDevices utils datasets
[9] methods base
other attached packages:
[1] statmod_1.4.24 sva_3.18.0 mgcv_1.8-11
[4] nlme_3.1-124 a4Base_1.18.0 gplots_2.17.0
[7] a4Core_1.18.0 a4Preproc_1.18.0 glmnet_2.0-2
[10] foreach_1.4.3 Matrix_1.2-3 multtest_2.26.0
[13] limma_3.26.7 genefilter_1.52.1 mpm_1.0-22
[16] KernSmooth_2.23-15 MASS_7.3-45 annaffy_1.42.0
[19] KEGG.db_3.2.2 GO.db_3.2.2 RSQLite_1.0.0
[22] DBI_0.3.1 AnnotationDbi_1.32.3 IRanges_2.4.6
[25] S4Vectors_0.8.11 Biobase_2.30.0 BiocGenerics_0.16.1
loaded via a namespace (and not attached):
[1] bitops_1.0-6 iterators_1.0.8 tools_3.2.2 annotate_1.48.0
[5] lattice_0.20-33 gtools_3.5.0 caTools_1.17.1 XML_3.98-1.3
[9] survival_2.38-3 gdata_2.17.0 codetools_0.2-14 splines_3.2.2
[13] xtable_1.8-0
Dear Aaron,
thank you for your quick response !!
So, i used
and it runned without an error !!