glmFit options in edgeR not passed to mglmLS?
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Davis, Wade ▴ 350
@davis-wade-2803
Last seen 9.6 years ago
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]]
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@gordon-smyth
Last seen 11 hours ago
WEHI, Melbourne, Australia
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}}
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