[BioC] glmFit options in edgeR not passed to mglmLS?

[Gordon K Smyth]

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
>

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