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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