Error while calling function topTable() from limma R package in microarray data analysis
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svlachavas ▴ 780
@svlachavas-7225
Last seen 7 weeks ago
Germany/Heidelberg/German Cancer Resear…

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    

limma microarray a4Core topTable statistical inference • 1.1k views
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Entering edit mode
Aaron Lun ★ 27k
@alun
Last seen 7 hours ago
The city by the bay

Try calling limma::topTable.

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Entering edit mode

Dear Aaron,

thank you for your quick response !!

So, i used 

top2 <- limma::topTable(fit3, coef="Meta_CancervsMeta_Control", number=nrow(fit3), adjust.method="fdr", sort.by="none")

and it runned without an error !!

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