Hi Kasia, Many thanks for the bug report, looks like a typo in our code that I'll correct. Regards, Mark On Fri, Jan 14, 2011 at 6:33 PM, Kasia Stepien <kasia at="" cmmt.ubc.ca=""> wrote: > Hi Mark, > > Thanks a lot! Nice that it is an easy fix. I also managed to get > around the problem by summarizing the BLData for each chip > independently, then combining them afterwards. > > Another bug in the beadarray package that I found when running > summarize, specific to ratv1 arrays, is that summarize looks for the > file 'ratv1BeadLevelMapping.rda', which does not exist in the library. > However, the file "ratBeadLevelMapping.rda" does, so we made a copy, > renamed it, and saved it in the directory, which seemed to solve the > problem temporarily. > >> BSData <- summarize(BLDataBsh, list(greenChannel), useSampleFac = FALSE) > No sample factor specified. Summarizing each section separately > Finding list of unique probes in beadLevelData > 23401 ?unique probeIDs found > Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection > In addition: Warning message: > In readChar(con, 5L, useBytes = TRUE) : > ?cannot open compressed file > '/usr/lib64/R/library/beadarray/extdata/ratv1BeadLevelMapping.rda', > probable reason 'No such file or directory' >> load("/usr/lib64/R/library/beadarray/extdata/ratBeadLevelMapping.rda") >> ratv1BeadLevelMapping<-ratBeadLevelMapping >> save(ratv1BeadLevelMapping, file="/usr/lib64/R/library/beadarray/ex tdata/ratv1BeadLevelMapping.rda") > > Cheers, > Kasia > > On Tue, Jan 11, 2011 at 8:19 AM, Mark Dunning <mark.dunning at="" gmail.com=""> wrote: >> Hi Kasla, >> >> This problem was due to some recent functionality added to beadarray. >> In short, the summarize function tries to be clever and work out which >> sections should be combined and renames columns accordingly It seems >> there was a bug that got the names confused when multiple chips are >> present in the bead-level object. >> >> For a simple fix for your data, if you try >> >>> BSData <- summarize(BLDataCombo, list(greenChannel),useSampleFac = FALSE) >> >> then it will not try this automatic grouping and naming of samples and >> you should get the column names you expect. In future the bug will >> have been fixed in the ?devel and release versions of beadarray. >> >> Best wishes, >> >> Mark >> >> On Fri, Jan 7, 2011 at 7:02 PM, Kasia Stepien <kasia at="" cmmt.ubc.ca=""> wrote: >>> Hello! >>> >>> I am using beadarray v 2.0.2 to analyze beadlevel data for Illumina >>> RatRef-12 whole genome gene expression arrays (I have 8 chips, with 12 >>> samples each, for a total of 96 arrays). >>> >>> When trying to create a bead summary object using "summarize", the >>> section names from the BLData object appear to be recycled (eg. >>> "5398636011_A", "5398636011_A.1", rather than "5398636011_A", >>> "5398636011_B", etc). At first I thought the arrays themselves were >>> being used reused, but the similarly named objects do not appear to be >>> identical (see below). >>> >>> What could the reason be for this? Is there some argument for >>> summarize that I can use to get around this problem? >>> >>> This is what it looks like for 2 chips, with 12 samples each: >>> >>>> BLData1 = readIllumina(dir="/home/kasia/kasiadata/5398636011filtered/", useImages=FALSE, illuminaAnnotation="Ratv1") >>> Processing section 5398636011_A >>> Processing section 5398636011_B >>> Processing section 5398636011_C >>> Processing section 5398636011_D >>> Processing section 5398636011_E >>> Processing section 5398636011_F >>> Processing section 5398636011_G >>> Processing section 5398636011_H >>> Processing section 5398636011_I >>> Processing section 5398636011_J >>> Processing section 5398636011_K >>> Processing section 5398636011_L >>>> BLData2 = readIllumina(dir="/home/kasia/kasiadata/5398636033filtered/", useImages=FALSE, illuminaAnnotation="Ratv1") >>> Processing section 5398636033_A >>> Processing section 5398636033_B >>> Processing section 5398636033_C >>> Processing section 5398636033_D >>> Processing section 5398636033_E >>> Processing section 5398636033_F >>> Processing section 5398636033_G >>> Processing section 5398636033_H >>> Processing section 5398636033_I >>> Processing section 5398636033_J >>> Processing section 5398636033_K >>> Processing section 5398636033_L >>>> BLDataCombo = combine(BLData1, BLData2) >>>> is(BLDataCombo) >>> [1] "beadLevelData" >>>> sectionNames(BLDataCombo) >>> ?[1] "5398636011_A" "5398636011_B" "5398636011_C" "5398636011_D" "5398636011_E" >>> ?[6] "5398636011_F" "5398636011_G" "5398636011_H" "5398636011_I" "5398636011_J" >>> [11] "5398636011_K" "5398636011_L" "5398636033_A" "5398636033_B" "5398636033_C" >>> [16] "5398636033_D" "5398636033_E" "5398636033_F" "5398636033_G" "5398636033_H" >>> [21] "5398636033_I" "5398636033_J" "5398636033_K" "5398636033_L" >>> >>>> myMean = function(x) mean(x, na.rm = TRUE) >>>> mySd = function(x) sd(x, na.rm = TRUE) >>>> greenChannel = new("illuminaChannel", logGreenChannelTransform, illuminaOutlierMethod, myMean, mySd, "G") >>>> BSData <- summarize(BLDataCombo, list(greenChannel)) >>>> str(exprs(BSData)) >>> ?num [1:23350, 1:24] 9.92 7.42 7.43 7.5 12.34 ... >>> ?- attr(*, "dimnames")=List of 2 >>> ?..$ : chr [1:23350] "ILMN_2039396" "ILMN_2040732" "ILMN_2039699" >>> "ILMN_2038916" ... >>> ?..$ : chr [1:24] "5398636011_A" "5398636033_B" "5398636011_C" >>> "5398636033_D" ... >>> >>>> colnames(exprs(BSData)) >>> ?[1] "5398636011_A" ? "5398636033_B" ? "5398636011_C" ? "5398636033_D" >>> ?[5] "5398636011_E" ? "5398636033_F" ? "5398636011_G" ? "5398636033_H" >>> ?[9] "5398636011_I" ? "5398636033_J" ? "5398636011_K" ? "5398636033_L" >>> [13] "5398636011_A.1" "5398636033_B.1" "5398636011_C.1" "5398636033_D.1" >>> [17] "5398636011_E.1" "5398636033_F.1" "5398636011_G.1" "5398636033_H.1" >>> [21] "5398636011_I.1" "5398636033_J.1" "5398636011_K.1" "5398636033_L.1" >>> >>>> identical(exprs(BSData)[,1],exprs(BSData)[,13]) >>> [1] FALSE >>> >>>> head(cbind(exprs(BSData)[,1],exprs(BSData)[,13])) >>> ? ? ? ? ? ? ? ? ?[,1] ? ? ?[,2] >>> ILMN_2039396 ?9.917607 ?9.817626 >>> ILMN_2040732 ?7.415167 ?7.436922 >>> ILMN_2039699 ?7.432883 ?7.423043 >>> ILMN_2038916 ?7.504111 ?7.619327 >>> ILMN_1374916 12.342863 13.377692 >>> ILMN_1353986 ?7.210915 ?7.211393 >>> >>> >>>> sessionInfo() >>> R version 2.12.0 (2010-10-15) >>> Platform: x86_64-redhat-linux-gnu (64-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] illuminaRatv1BeadID.db_1.8.0 org.Rn.eg.db_2.4.6 >>> [3] RSQLite_0.9-2 ? ? ? ? ? ? ? ?DBI_0.2-5 >>> [5] AnnotationDbi_1.12.0 ? ? ? ? beadarray_2.0.2 >>> [7] Biobase_2.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] KernSmooth_2.23-4 limma_3.4.5 ? ? ? tools_2.12.1 >>> >>> >>> >>> Thank you! >>> Kasia >>> >>> -- >>> Kasia Stepien, M.Sc. Candidate >>> Department of Medical Genetics >>> University of British Columbia >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > > > > -- > Kasia Stepien, M.Sc. Candidate > Department of Medical Genetics > University of British Columbia >