Entering edit mode
Hi Marcus,
I haven't seen this problem myself. I've just tried running the
Weaver
case study in the limma User's Guide, and it still runs correctly for
me,
using either R 2.15.1 or R-devel on Windows.
There weren't any changes to that part of the limma code between R
2.14.1
and R 2.15.1, so the change you are seeing may be in the stats
package.
Best wishes
Gordon
---------------- original message ---------------
[BioC] Limma normalization error and loess.R segmentation type fault
(windows)
Marcus Davy mdavy86 at gmail.com
Tue Sep 4 07:11:43 CEST 2012
Is anyone having recent problems after upgrading to R-2.15.1 on
windows
with limma or other bioconductor packages that use loess functions in
the
stats core package.?
The normalization function normalizeWithinArrays(...,
method=printtiploess) is crashing on two independent windows machines
since upgrading R from 2.14.1 to 2.15.1 using the stable release
packages
on bioconductor. I have a segmentation type fault of Rgui.exe running
this
code snippet;
system.time(MA <- normalizeWithinArrays(RG, method="printtiploess",
bc.method="none"))
Process R exited abnormally with code 148 at Tue Sep 04 14:42:30 2012
I can get a more meaningful error if I install the development release
of
limma;
useDevel()
biocLite("limma")
system.time(MA <- normalizeWithinArrays(RG, method="printtiploess",
bc.method="none"))
Error in stats:::simpleLoess(y = yobs, x = xobs, weights = wobs, span
=
span, :
NA/NaN/Inf in foreign function call (arg 1)
Timing stopped at: 12.34 2.11 14.5
The number of NAs and weights in the offending array are;
> sumis.na(tmp$M))
[1] 717
> sumis.na(tmp$A))
[1] 717
> table(tmp$weights)
0 1
8362 10070
The error appears to be caused in R core->stats:::simpleLoess (not
limma)
when interfacing C code, and I can see there have been recent commits
to
the stats/loess.R file in the R core subversion repository. In the
stable
release, limma calls normalizeWithinArrays() -> loessFit() >
.vsimpleLoess(), which appear to have modified to
normalizeWithinArrays() -> loessFit() > stats:::simpleLoess in the
development release of limma, which explains the error I get with the
development release of limma.
A colleague independently tested normalizing the one offending
microarray
slide I identified causing the same segmentation type fault on his
machine, Sorry I have not provided a reproducible example but I can
provide an RSave to load just that array of data, and the code
snippets to
reproduce the error in an email, this bug appears to be data
dependent,
windows dependent (my example code works fine without crashing on
linux
using R version 2.15.0 and limma 3.12.0) and probably infrequent to
achieve.
cheers,
Marcus
## Stable release
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_New Zealand.1252 LC_CTYPE=English_New
Zealand.1252
[3] LC_MONETARY=English_New Zealand.1252 LC_NUMERIC=C
[5] LC_TIME=English_New Zealand.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biobase_2.16.0 BiocGenerics_0.2.0 limma_3.12.1
## development release
sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_New Zealand.1252 LC_CTYPE=English_New
Zealand.1252
[3] LC_MONETARY=English_New Zealand.1252 LC_NUMERIC=C
[5] LC_TIME=English_New Zealand.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.13.17
______________________________________________________________________
The information in this email is confidential and
intend...{{dropped:4}}
