dear all, I am using lumi to normalize raw Illumina Data, but when I run the script, I retrive this error. can you help me? library(lumi) r=lumiR("gene_expression.txt") b=lumiB(r, method="bgAdjust") Perform bgAdjust background correction ... There is no control probe information in the LumiBatch object! No background adjustment will be performed. thank you [[alternative HTML version deleted]]

On Tue, Nov 4, 2008 at 6:04 AM, John Lande <john.lande77@gmail.com> wrote: > dear all, > > I am using lumi to normalize raw Illumina Data, but when I run the script, > I > retrive this error. can you help me? > > library(lumi) > > r=lumiR("gene_expression.txt") > > b=lumiB(r, method="bgAdjust") > > Perform bgAdjust background correction ... > There is no control probe information in the LumiBatch object! > No background adjustment will be performed. > Hi, John. The lumi package needs control probe information to do background adjustment. It appears that your gene_expression.txt does not include the control probes. Also, I think this is just a warning, so you can probably proceed with your analysis either way. Finally, when posting to the list, remember to include sessionInfo(). Sean [[alternative HTML version deleted]]

On Tue, Nov 4, 2008 at 12:04 PM, John Lande <john.lande77@gmail.com> wrote: > dear all, > > I am using lumi to normalize raw Illumina Data, but when I run the script, > I retrive this error. can you help me? > > library(lumi) > > r=lumiR("gene_expression.txt") > > b=lumiB(r, method="bgAdjust") > > Perform bgAdjust background correction ... > There is no control probe information in the LumiBatch object! > No background adjustment will be performed. > > thank you > maybe it is just a problem of annotation, thereby I added the library annotation when I import data: > r=lumiR("Breast_86.txt", lib = "lumiHumanIDMapping.db") Annotation columns are not available in the data. Perform Quality Control assessment of the LumiBatch object ... Error in names(mapping.new) <- inputID.bak : 'names' attribute [24354] must be the same length as the vector [24350] but again another error... [[alternative HTML version deleted]]

Hi John, What's your sessionInfo()? The latest release version should be 1.8.2. If it is not, please update it. Tell me more details if there is any further problem. Pan On 11/5/08 6:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Date: Tue, 4 Nov 2008 14:45:06 +0100 > From: "John Lande" <john.lande77 at="" gmail.com=""> > Subject: Re: [BioC] Lumi Error > To: bioconductor at stat.math.ethz.ch > Message-ID: > <c2ebc3880811040545x2ade67beoecf6b6b36367b6f2 at="" mail.gmail.com=""> > Content-Type: text/plain > > On Tue, Nov 4, 2008 at 12:04 PM, John Lande <john.lande77 at="" gmail.com=""> wrote: > >> dear all, >> >> I am using lumi to normalize raw Illumina Data, but when I run the script, >> I retrive this error. can you help me? >> >> library(lumi) >> >> r=lumiR("gene_expression.txt") >> >> b=lumiB(r, method="bgAdjust") >> >> Perform bgAdjust background correction ... >> There is no control probe information in the LumiBatch object! >> No background adjustment will be performed. >> >> thank you >> > > maybe it is just a problem of annotation, thereby I added the library > annotation when I import data: > >> r=lumiR("Breast_86.txt", lib = "lumiHumanIDMapping.db") > Annotation columns are not available in the data. > Perform Quality Control assessment of the LumiBatch object ... > Error in names(mapping.new) <- inputID.bak : > 'names' attribute [24354] must be the same length as the vector [24350] > > but again another error... > > [[alternative HTML version deleted]] > > > > ------------------------------ > > Message: 13 > Date: Tue, 4 Nov 2008 08:54:54 -0500 > From: "Sean Davis" <sdavis2 at="" mail.nih.gov=""> > Subject: Re: [BioC] Lumi Error > To: "John Lande" <john.lande77 at="" gmail.com=""> > Cc: bioconductor at stat.math.ethz.ch > Message-ID: > <264855a00811040554n7c45c42fva93e627b8e8fe586 at mail.gmail.com> > Content-Type: text/plain > > On Tue, Nov 4, 2008 at 8:45 AM, John Lande <john.lande77 at="" gmail.com=""> wrote: > >> On Tue, Nov 4, 2008 at 12:04 PM, John Lande <john.lande77 at="" gmail.com=""> >> wrote: >> >>> dear all, >>> >>> I am using lumi to normalize raw Illumina Data, but when I run the >> script, >>> I retrive this error. can you help me? >>> >>> library(lumi) >>> >>> r=lumiR("gene_expression.txt") >>> >>> b=lumiB(r, method="bgAdjust") >>> >>> Perform bgAdjust background correction ... >>> There is no control probe information in the LumiBatch object! >>> No background adjustment will be performed. >>> >>> thank you >>> >> >> maybe it is just a problem of annotation, thereby I added the library >> annotation when I import data: >> > > No. It is that you did not include control probe information in the > exported data from beadstudio, so lumi has no idea what the background is. > > >> >>> r=lumiR("Breast_86.txt", lib = "lumiHumanIDMapping.db") >> Annotation columns are not available in the data. >> Perform Quality Control assessment of the LumiBatch object ... >> Error in names(mapping.new) <- inputID.bak : >> 'names' attribute [24354] must be the same length as the vector [24350] >> >> but again another error... >> > > You'll need to determine the annotation package that goes with your chip. > For illumina, there are a number of choices, so you'll have to choose the > right one based on the chip and the ID that you want to map. The > lumiHumanIDMapping.db package simply maps between different human chips and > does not provide annotation. What you have tried here cannot work. > > Sean > > [[alternative HTML version deleted]] > >