Hi, I've been trying to follow some of the QC steps listed on "Analysis of Bead-level Data using beadarray" (dated October 23, 2010) Seems like BLData variable is hardcoded: >library(beadarray) >ar1 = readIllumina(dir = "4849554032", useImages = FALSE, illuminaAnnotation = "Humanv3", metricsFile = "Metrics.txt") ..... > boxplot(ar1, las = 2, outline = FALSE, ylim = c(4,12), main = "Green Foreground") Error in getBeadData(BLData, array = array, what = "Grn") : object 'BLData' not found > boxplot(BLData=ar1, las = 2, outline = FALSE, ylim = c(4,12), main = "Green Foreground") Error in list(x, ...) : 'x' is missing > BLData = ar1 > boxplot(BLData) #this works Thanks, Ying Wu > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i486-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] beadarray_2.0.1 Biobase_2.10.0 loaded via a namespace (and not attached): [1] limma_3.6.4 tcltk_2.12.0 tools_2.12.0 [[alternative HTML version deleted]]

Hi, Thank you for reporting this bug. We detected it ourselves a few days ago and it was patched in beadarray 2.0.2. If you run update.packages() or download the latest version of beadarray the problem should no longer be present. Many thanks ------------------------------------------------ Mike Smith PhD Student Computational Biology Group Cambridge University On Wed, Nov 3, 2010 at 9:21 PM, Ying W <daiyingw@gmail.com> wrote: > Hi, > I've been trying to follow some of the QC steps listed on "Analysis of > Bead-level Data using beadarray" (dated October 23, 2010) > Seems like BLData variable is hardcoded: > > >library(beadarray) > >ar1 = readIllumina(dir = "4849554032", useImages = FALSE, > illuminaAnnotation = "Humanv3", metricsFile = "Metrics.txt") > ..... > > boxplot(ar1, las = 2, outline = FALSE, ylim = c(4,12), main = "Green > Foreground") > Error in getBeadData(BLData, array = array, what = "Grn") : > object 'BLData' not found > > boxplot(BLData=ar1, las = 2, outline = FALSE, ylim = c(4,12), main = > "Green Foreground") > Error in list(x, ...) : 'x' is missing > > BLData = ar1 > > boxplot(BLData) #this works > > Thanks, > Ying Wu > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i486-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] beadarray_2.0.1 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] limma_3.6.4 tcltk_2.12.0 tools_2.12.0 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hi, Thanks for the report. I noticed the bug and thought it should have been fixed in beadarray 2.0.1. The only the thing I can suggest is try to update again (latest version is 2.0.2) and see if the bug still appears. Regards, Mark On Wed, Nov 3, 2010 at 9:21 PM, Ying W <daiyingw at="" gmail.com=""> wrote: > Hi, > I've been trying to follow some of the QC steps listed on "Analysis of > Bead-level Data using beadarray" (dated October 23, 2010) > Seems like BLData variable is hardcoded: > >>library(beadarray) >>ar1 = readIllumina(dir = "4849554032", useImages = FALSE, > illuminaAnnotation = "Humanv3", metricsFile = "Metrics.txt") > ..... >> boxplot(ar1, las = 2, outline = FALSE, ylim = c(4,12), main = "Green > Foreground") > Error in getBeadData(BLData, array = array, what = "Grn") : > ?object 'BLData' not found >> boxplot(BLData=ar1, las = 2, outline = FALSE, ylim = c(4,12), main = > "Green Foreground") > Error in list(x, ...) : 'x' is missing >> BLData = ar1 >> boxplot(BLData) #this works > > Thanks, > Ying Wu > >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i486-pc-linux-gnu (32-bit) > > locale: > ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C > ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 > ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 > ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] beadarray_2.0.1 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] limma_3.6.4 ?tcltk_2.12.0 tools_2.12.0 > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >