Question: Error while calling function topTable() from limma R package in microarray data analysis
0
gravatar for svlachavas
3.3 years ago by
svlachavas660
Greece/Athens/National Hellenic Research Foundation
svlachavas660 wrote:

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    

ADD COMMENTlink modified 3.3 years ago by Aaron Lun23k • written 3.3 years ago by svlachavas660
Answer: Error while calling function topTable() from limma R package in microarray data
2
gravatar for Aaron Lun
3.3 years ago by
Aaron Lun23k
Cambridge, United Kingdom
Aaron Lun23k wrote:

Try calling limma::topTable.

ADD COMMENTlink written 3.3 years ago by Aaron Lun23k

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 !!

ADD REPLYlink written 3.3 years ago by svlachavas660
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 193 users visited in the last hour