Hello
Thanks a lot Marc, for the suggestion to explore the issue a bit more
systematically
So I did and the conclusion is that with the old drc 1.4-2, I get a
SE=0.003, with the new drc 1.5-2, I get a SE=0.4
irrespective of the R version or the version of the packages drc depends
on
I hope somebody can help me further, I still have the feeling that a SE
of 0.003 on an IC50 of 1.2, for a reasonable good fit is more realistic
than a SE of 0.4 on an IC50 of 1.2
Regards,
Hans
Here are the results of the following test script:
d<-data.frame(dose=c(2.00e-05,4.00e-06,8.00e-07,1.60e-07,3.20e-08,6.40e-
09,1.28e-09,2.56e-10,5.10e-11,1.00e-11,2.00e-05,4.00e-06,8.00e-07,1.60e-
07,3.20e-08,6.40e-09,1.28e-09,2.56e-10,5.10e-11,1.00e-11),response=c(97.
202,81.670,47.292,16.924, 16.832, 6.832, 11.118, 1.319, 5.495,
-3.352, 102.464, 83.114, 50.631, 22.792, 18.348, 19.066, 27.794,
14.682, 11.992, 12.868))
m<- drm(response ~ (log10(dose*1e6)), data = d, fct = l4(fixed =
c(NA,NA,NA,NA), names = c("hs", "bottom", "top", "ec50")), logDose = 10,
control = drmc(useD = T))
summary(m)
RESULTS:
sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32
locale:
LC_COLLATE=Dutch_Belgium.1252;LC_CTYPE=Dutch_Belgium.1252;LC_MONETARY=Du
tch_Belgium.1252;LC_NUMERIC=C;LC_TIME=Dutch_Belgium.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] drc_1.5-2 plotrix_2.4-2 nlme_3.1-89 MASS_7.2-41
lattice_0.17-6
[6] alr3_1.1.7
loaded via a namespace (and not attached):
[1] grid_2.7.0 tools_2.7.0
RESULT: ec50:(Intercept)=1.27447 SE=0.43541
CONCLUSION: R 2.7.0 with recent drc 1.5-2 (older dependencies) gives
SE=0.43541
========================================================================
=======
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
LC_COLLATE=Dutch_Belgium.1252;LC_CTYPE=Dutch_Belgium.1252;LC_MONETARY=Du
tch_Belgium.1252;LC_NUMERIC=C;LC_TIME=Dutch_Belgium.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] drc_1.4-2 plotrix_2.5-5 nlme_3.1-90 MASS_7.2-46
[5] lattice_0.17-22 alr3_1.1.7
loaded via a namespace (and not attached):
[1] grid_2.9.0 tools_2.9.0
RESULT: ec50:(Intercept) SE=1.2039e+00
CONCLUSION: R 2.9.0 with old drc 1.4-2 (newer dependencies) gives
SE=0.003
Hans,
You have three important factors changing here. The version of R, the
version of drc and the versions of any relevant drc dependencies
(alr3, lattice, magic, MASS, nlme, plotrix).
I would first try to install the newer version of drc on the older R
system (all else staying the same) and see what you get. Don't run
update.packages() here, lest you change other things. Just install the
newer version of drc.
If you get the same results as the older version, then it might lead
you to something in R or one of the package dependencies changing.
If you get a different result, then it would lead to something in drc
changing.
You can also install the old version of drc on your more recent R
system to see what you get, which might help to confirm behavior.
The old source version of drc would be available from:
http://cran.r-project.org/src/contrib/Archive/drc/
I also found a Windows binary of the old package here:
http://cran.r-project.org/bin/windows/contrib/2.6/drc_1.4-2.zip
I have also copied Christian Ritz, the drc package author/maintainer,
so that he may be able to assist you further with the problem.
HTH,
Marc Schwartz
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