Thanks for reporting the problem! Alice. The current hist method in lumi package was not allowed to change lty parameters. I have changed the function and make it user changeable. Pan Du On 9/5/07 4:55 PM, "Wolfgang Huber" <huber at="" ebi.ac.uk=""> wrote: > [BioC] lty argument not recognised in plot function > Data: Wed, 5 Sep 2007 15:07:53 +1200 > Da: Johnstone, Alice <alice.johnstone at="" esr.cri.nz=""> > A: <bioconductor at="" stat.math.ethz.ch=""> > > Hi > Trying to produce a histogram with the same line type for each sample > but it produces the error below: > >> hist(data.lumi,col=cols,lty=1) > Error in matplot(all.x, all.y, ylab = ylab, xlab = xlab, type = type, : > > formal argument "lty" matched by multiple actual arguments > > >> sessionInfo() > R version 2.6.0 Under development (unstable) (2007-08-11 r42469) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New > Zealand.1252;LC_MONETARY=English_New > Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > > [8] base > > other attached packages: > [1] lumiRatV1_1.3.0 lumi_1.3.29 annotate_1.15.3 > > [4] AnnotationDbi_0.0.88 RSQLite_0.6-0 DBI_0.2-3 > > [7] mgcv_1.3-25 affy_1.15.7 > preprocessCore_0.99.12 > [10] affyio_1.5.8 Biobase_1.15.26 > > > This has previously worked for me, so has something changed in the devel > package that I need to alter my script? > Cheers > Alice

Thank you! When will the update be available? Will you also be able to change colours in plots also? I am comparing Illumina data to Affymetrix data so the similar I can make the outputs the better! Also is it possible to compare Illumina data MA plots to a pseudo median reference, rather than pairwise? -----Original Message----- From: Pan Du [mailto:dupan@northwestern.edu] Sent: Thursday, 6 September 2007 11:21 a.m. To: Johnstone, Alice; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] lty argument not recognised in plot function] Thanks for reporting the problem! Alice. The current hist method in lumi package was not allowed to change lty parameters. I have changed the function and make it user changeable. Pan Du On 9/5/07 4:55 PM, "Wolfgang Huber" <huber at="" ebi.ac.uk=""> wrote: > [BioC] lty argument not recognised in plot function > Data: Wed, 5 Sep 2007 15:07:53 +1200 > Da: Johnstone, Alice <alice.johnstone at="" esr.cri.nz=""> > A: <bioconductor at="" stat.math.ethz.ch=""> > > Hi > Trying to produce a histogram with the same line type for each sample > but it produces the error below: > >> hist(data.lumi,col=cols,lty=1) > Error in matplot(all.x, all.y, ylab = ylab, xlab = xlab, type = type, : > > formal argument "lty" matched by multiple actual arguments > > >> sessionInfo() > R version 2.6.0 Under development (unstable) (2007-08-11 r42469) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New > Zealand.1252;LC_MONETARY=English_New > Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > > [8] base > > other attached packages: > [1] lumiRatV1_1.3.0 lumi_1.3.29 annotate_1.15.3 > > [4] AnnotationDbi_0.0.88 RSQLite_0.6-0 DBI_0.2-3 > > [7] mgcv_1.3-25 affy_1.15.7 > preprocessCore_0.99.12 > [10] affyio_1.5.8 Biobase_1.15.26 > > > This has previously worked for me, so has something changed in the > devel package that I need to alter my script? > Cheers > Alice P Think before you print This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed. If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you.