DESeq baseVarFunc is not working

[jay2008]

can you help me to make function "baseVarFunc" below (from supplementary 2 of DESeq paper) work?
I got error:
Error in baseVarFunc(cdsFly, "A")(10^xg) : could not find function "rvf"

here is the code (file fly_RNA_counts.tsv was downloaded from supplementary 3).




baseVarFunc <- function( cds, cond ) {
rvf <- rawVarFunc( cds, cond )
sf <- sizeFactors(cds)[ conditions(cds) == cond ]
xim <- sum(1/sf) / length(sf)
function( q ) rvf( q ) + xim * q
}

rawVarFunc <- function( cds, condOrName ) {
stopifnot( is( cds, "CountDataSet" ) )
res <- cds@fitInfo[[ as.character(condOrName) ]]
if( is.null(res) ) {
res <- cds@fitInfo[[ cds@dispTable[ as.character(condOrName) ] ]]
if( is.null(res) )
stop( sprintf( "No base variance function found for condition or with name '%s'.", condOrName ) )
}
res
}


countsTableFly <- read.delim( "fly_RNA_counts.tsv" )
condsFly <- c( "A", "A", "B", "B" )
rownames( countsTableFly ) <- paste( "Gene", 1:nrow(countsTableFly), sep="_" )
cdsFly <- newCountDataSet( countsTableFly, condsFly )
cdsFly <- estimateSizeFactors( cdsFly )
cdsFly <- estimateDispersions( cdsFly )
gg<-log10( baseVarFunc(cdsFly,"A")( 10^xg ) ) ## this sentence got error


> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] DESeq_1.22.1 lattice_0.20-33 locfit_1.5-9.1 Biobase_2.30.0 BiocGenerics_0.16.1

loaded via a namespace (and not attached):
[1] IRanges_2.4.7 XML_3.98-1.3 grid_3.2.3 xtable_1.8-2 DBI_0.3.1
[6] stats4_3.2.3 RSQLite_1.0.0 genefilter_1.52.1 annotate_1.48.0 S4Vectors_0.8.11
[11] splines_3.2.3 RColorBrewer_1.1-2 geneplotter_1.48.0 survival_2.38-3 AnnotationDbi_1.32.3

[dpryan]

Why are you trying to use DESeq? It's out dated and shouldn't be used for new projects (that's what DESeq2 is for).

[jay2008]

I am going to investigate the difference between DESeq and DESeq2. the reason is that I can better understand the advantages of DESeq2 by reading, testing original DESeq.
you are right, as a user, who should simply pick up better tool, but I want to know more about DESeq than a normal user. if you can solve the problem, it will be great appreciated. thanks
Jay

[dpryan]

It looks like that part was in error and I'm not familiar enough with how the 2010 version of DESeq worked internally to be able to reverse engineer things quickly. I would suggest just skipping that and following the vignette and user guide of the most recent version.

[jay2008]

thanks, the code is from supplementary 2. actually, i try to do it work in current DESeq version.
can anyone else help this issue?

[Wolfgang Huber]

The original post was cross-posted, and is answered here: https://support.bioconductor.org/p/78427/#78550