Thank you. The chips used for my experiment were the RatRef-12 expression beadchips. -----Original Message----- From: Matt Ritchie [mailto:Matt.Ritchie@cancer.org.uk] Sent: Saturday, 1 March 2008 3:36 a.m. To: Johnstone, Alice Cc: bioconductor Subject: Re: [BioC] Help for readIllumina beadlevel error Hi Alice, Thanks for your email. This is a bug, which should be fixed in beadarray 1.7.4. Most arrays we see (those from SAMs and WG6 chips) are named using the convention chipID_row_column, and this information is stored along with other processing options in the arrayInfo slot of a BeadLevelList. Your arrays look to be named as chipID_row, and when readIllumina() attempts to store something for column, you get the error below. I guess this naming convention is used for human/mouse 8 arrays? Best wishes, Matt > Hi > I want to read in each array at beadlevel separately, but when I do > this I get the following error: > >> > B13Data<-readIllumina(arrayNames=c("4194720030_F"),textType=".txt",bac > kg > roundMethod > + > ="none",offset=0,normalizeMethod="none",metrics=FALSE,useImages=TRUE,t > ar > gets=targets) > Found 1 arrays > Error in seq.default(3, length(tmp), by = 3) : > wrong sign in 'by' argument > >> sessionInfo() > R version 2.6.2 (2008-02-08) > 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] illuminaRatBCv1_1.1.0 beadarray_1.6.0 affy_1.16.0 > [4] preprocessCore_1.0.0 affyio_1.6.1 geneplotter_1.16.0 > [7] lattice_0.17-4 annotate_1.16.1 xtable_1.5-2 > [10] AnnotationDbi_1.0.6 RSQLite_0.6-7 DBI_0.2-4 > [13] Biobase_1.16.3 limma_2.12.0 > > loaded via a namespace (and not attached): > [1] grid_2.6.2 KernSmooth_2.22-22 RColorBrewer_1.0-2 > > > > Can someone explain what I've done wrong? > Thanks! > > > > Alice Johnstone 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.