Hi Alice, When I added the detection="Detection"as you suggested as in, > BSData <- readBeadSummaryData( dataFile, skip = 7, columns = list( exprs = "AVG_Signal", se.exprs = "BEAD_STDEV", NoBeads = "Avg_NBEADS", detection = "Detection" ), annoPkg = "lumiRatV1" ) I now get the following error message: > Did not find a slot called : detection This is where I am confused a bit. You see, according the readBeadSummaryData help file, the default slot name is 'Detection' not 'detection', however, the call to > BSData.lumi <- normaliseIllumina(BSData, method = "quantile", transform = "vst") is looking for the slot name 'detection', which doesn't exist because readBeadSummaryData() wants the slot name to be 'Detection'. Is there a way to rename the slot name in the BSData object from 'Detection' to 'detection'? Thanks for your help! Elliot Johnstone, Alice wrote: > You just need to add the detection="Detection" to the list of columns in > the readBeadSummaryData command so that it reads this column of your > data also. > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Elliot > Kleiman > Sent: Thursday, 10 January 2008 11:55 a.m. > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] About beadarray normaliseIllumina() warning messages > > Hi BioC list, > > In package beadarray, when I call function normaliseIllumina() with > arguments [method = "quantile", transform = "vst"] I get the following > warning messages: > > Warning messages: > 1: In detectionCall(x.lumi, Th = 0.01, type = "matrix") : > No detection slot found! > 2: In rm(list = c("se.exprs", "detection", "beadNum"), envir = aData) : > variable "detection" was not found > > [Question(s)]: > * Does that mean it's still doing what its supposed to be doing? (Or is > it bailing out returning these warnings messages instead?) > * I am wondering if its safe to simply ignore these warnings? > > Here's a snippet of my raw bead summary header-info: > --- > Illumina Inc. BeadStudio version 2.3.47 > Normalization = none > Array Content = RatRef_12_v1_11222119_A.xml.xml Error Model = none > DateTime = 7/12/2007 12:18 PM Local Settings = en-US > > TargetID MIN_Signal AVG_Signal MAX_Signal NARRAYS > ARRAY_STDEV BEAD_STDEV Avg_NBEADS Detection > --- > > For example, when I go to read in my raw bead summary data and vst > transform with quantile normalization, I do: > > > # load packages > > library(beadarray) > > library(lumi) > > library(lumiRatV1) > > # read-in raw bead summary data > > # create BSData object > > BSData <- readBeadSummaryData( dataFile, > skip = 7, > columns = list( exprs = "AVG_Signal", > se.exprs = "BEAD_STDEV", > NoBeads = "Avg_NBEADS" > ), > annoPkg = "lumiRatV1" > ) > > # perform lumi vst transformation and quantile normalization > > BSData.lumi <- normaliseIllumina(BSData, method = "quantile", transform > = "vst") > 2008-01-09 13:54:12 , processing array 1 ... > 2008-01-09 13:54:21 , processing array 48 Warning messages: > 1: In detectionCall(x.lumi, Th = 0.01, type = "matrix") : > No detection slot found! > 2: In rm(list = c("se.exprs", "detection", "beadNum"), envir = aData) : > variable "detection" was not found > > Thank you, > > Elliot Kleiman > > > # print sessionInfo > > sessionInfo() > R version 2.6.1 (2007-11-26) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=e n_US > ;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHON E=C; > LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] beadarray_1.6.0 geneplotter_1.16.0 lattice_0.17-2 > [4] maSigPro_1.10.0 lumiRatV1_1.3.1 estrogen_1.8.2 > [7] vsn_3.2.1 hgu95av2cdf_2.0.0 hgu95av2_2.0.1 > [10] limma_2.12.0 lumi_1.4.0 annotate_1.16.1 > [13] xtable_1.5-2 AnnotationDbi_1.0.6 RSQLite_0.6-4 > [16] DBI_0.2-4 mgcv_1.3-29 affy_1.16.0 > [19] preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.2 > > loaded via a namespace (and not attached): > [1] KernSmooth_2.22-21 RColorBrewer_1.0-2 grid_2.6. > > -- > __________________________ > MS graduate student > Program in Computational Science > San Diego State University > http://www.csrc.sdsu.edu/ > > _______________________________________________ > 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 > > 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. > > > > -- __________________________ MS graduate student Program in Computational Science San Diego State University http://www.csrc.sdsu.edu/