Dear Gordon and Davis, I tried passing maxit to mglmLS when using glmFit via the following code, and I get this message: >fit.filt.tgw <- glmFit(y=dge.filt.tgw, design=rip.design,maxit = 100) Error in glmFit(y = dge.filt.tgw, design = rip.design, maxit = 100) : unused argument(s) (maxit = 100) Everything works fine when maxit is removed from the call. Also note that the method used is linesearch: fit.filt.tgw <- glmFit(y=dge.filt.tgw, design=rip.design) > fit.filt.tgw$method [1] "linesearch" The help page for glmFit reads "... other arguments are passed to lower-level functions, for example to mglmLS. Looking inside glmFit.default, everything looks fine to me: fit <- switch(method, linesearch = mglmLS(y, design = design, dispersion = dispersion, start = start, offset = offset, ...), oneway = mglmOneWay(y, design = design, dispersion = dispersion, offset = offset), levenberg = mglmLevenberg(y, design = design, dispersion = dispersion, offset = offset), simple = mglmSimple(y, design = design, dispersion = dispersion, offset = offset, weights = weights)) To make sure that mglmLS is using linesearch I made the call as but got the same result: > fit.filt.tgw <- glmFit(y=dge.filt.tgw, design=rip.design, method="linesearch", maxit = 100) Error in glmFit(y = dge.filt.tgw, design = rip.design, method = "linesearch", : unused argument(s) (maxit = 100) Calling mglmLS directly works (although I know it isn't intended to be called this way): temp<-mglmLS (y=as.matrix(dge.filt.tgw), design=rip.design, maxit = 50, # also used maxit=100 with no problem dispersion= dge.filt.tgw$tagwise.dispersion) Am I doing something wrong? Thanks, Wade > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) 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] stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.14.4 latticeExtra_0.6-23 RColorBrewer_1.0-5 Rsamtools_1.8.5 [5] lattice_0.20-8 Biostrings_2.24.1 GenomicRanges_1.8.6 IRanges_1.14.3 [9] BiocGenerics_0.2.0 plyr_1.7.1 edgeR_2.6.7 limma_3.12.1 loaded via a namespace (and not attached): [1] Biobase_2.16.0 bitops_1.0-4.1 grid_2.15.0 hwriter_1.3 stats4_2.15.0 tools_2.15.0 [7] zlibbioc_1.2.0 [[alternative HTML version deleted]]

Dear Wade, Thanks very much for the bug report. The "..." argument was missing in the generic function, although it is correct in the methods. I've committed a fix today. You should be able to install the updated edgeR from Bioconductor within a couple of days. Best wishes Gordon > From: Davis, Wade > Sent: Thursday, June 14, 2012 11:15 AM > To: bioconductor at r-project.org > Subject: glmFit options in edgeR not passed to mglmLS? > > Dear Gordon and Davis, > I tried passing maxit to mglmLS when using glmFit via the following code, and I get this message: > >> fit.filt.tgw <- glmFit(y=dge.filt.tgw, design=rip.design,maxit = 100) > > Error in glmFit(y = dge.filt.tgw, design = rip.design, maxit = 100) : > unused argument(s) (maxit = 100) > > Everything works fine when maxit is removed from the call. Also note that the method used is linesearch: > > fit.filt.tgw <- glmFit(y=dge.filt.tgw, design=rip.design) > >> fit.filt.tgw$method > [1] "linesearch" > > The help page for glmFit reads > ?... > > other arguments are passed to lower-level functions, for example to mglmLS. > > > Looking inside glmFit.default, everything looks fine to me: > > fit <- switch(method, linesearch = mglmLS(y, design = design, > dispersion = dispersion, start = start, offset = offset, > ...), oneway = mglmOneWay(y, design = design, dispersion = dispersion, > offset = offset), levenberg = mglmLevenberg(y, design = design, > dispersion = dispersion, offset = offset), simple = mglmSimple(y, > design = design, dispersion = dispersion, offset = offset, > weights = weights)) > > To make sure that mglmLS is using linesearch I made the call as but got the same result: > >> fit.filt.tgw <- glmFit(y=dge.filt.tgw, design=rip.design, method="linesearch", maxit = 100) > Error in glmFit(y = dge.filt.tgw, design = rip.design, method = "linesearch", : > unused argument(s) (maxit = 100) > > Calling mglmLS directly works (although I know it isn?t intended to be called this way): > > temp<-mglmLS (y=as.matrix(dge.filt.tgw), > design=rip.design, > maxit = 50, # also used maxit=100 with no problem > dispersion= dge.filt.tgw$tagwise.dispersion) > > Am I doing something wrong? > > Thanks, > Wade > >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > 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] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.14.4 latticeExtra_0.6-23 RColorBrewer_1.0-5 Rsamtools_1.8.5 > [5] lattice_0.20-8 Biostrings_2.24.1 GenomicRanges_1.8.6 IRanges_1.14.3 > [9] BiocGenerics_0.2.0 plyr_1.7.1 edgeR_2.6.7 limma_3.12.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.16.0 bitops_1.0-4.1 grid_2.15.0 hwriter_1.3 stats4_2.15.0 tools_2.15.0 > [7] zlibbioc_1.2.0 > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:5}}