Question

beadarray - can't load data

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Zoe.VanHavre@student.griffith.edu.au ▴ 10

@zoevanhavrestudentgriffitheduau-2938

Last seen 9.6 years ago

Hi, I want trying to do background correction to a Beastudio output file but I can't read it into beadarray. The sample file (.txt) has the following header: Illumina Inc. BeadStudio version 3.1.7 Normalization = none Array Content = HumanRef-8_V2_0_R0_11223162_A.bgx.xml Error Model = none DateTime = 24/09/2007 3:01 PM Local Settings = en-AU ProbeID TargetID ...etc The R code used and error message: PD.bstudiofile ='PD Vs Controls Only (n=70)_Sample_Probe_Profile_Nicko edit.txt' sampleSheet = "HumanRef-8_V2_11223162_B.csv" PD<-readBeadSummaryData( dataFile=PD.bstudiofile, sampleSheet=sampleSheet, skip=7, ProbeID="ProbeID", columns = list( exprs = "AVG_Signal", NoBeads = "Avg_NBEADS", Detection="Detection", BeadStDev="BEAD_STDEV")) Error in assayData(BSData)[[index]] = as.matrix(data[[i]]) : attempt to select less than one element I've checked everything, tried different skip values, etc, with no luck! Please help me get this data loaded! sample information is sessionInfo() R version 2.7.1 (2008-06-23) i486-pc-linux-gnu attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] beadarray_1.8.0 affy_1.18.2 preprocessCore_1.2.0 [4] affyio_1.8.0 geneplotter_1.18.0 annotate_1.18.0 [7] xtable_1.5-2 AnnotationDbi_1.2.2 RSQLite_0.6-9 [10] DBI_0.2-4 lattice_0.17-10 Biobase_2.0.1 [13] limma_2.14.5 thanks in advance for your advice Zoe van Havre Griffith University [[alternative HTML version deleted]]

beadarray beadarray • 816 views

ADD COMMENT • link updated 15.7 years ago by Matt Ritchie ▴ 460 • written 15.8 years ago by Zoe.VanHavre@student.griffith.edu.au ▴ 10

score 0 · Answer 1 · 2008-07-24

Hi Zoe, There are a few things you could look at. 1. Check the columns argument in readBeadSummaryData(). I think it should be columns=list(exprs = "AVG_Signal", ??? ??? ??? ???NoBeads = "Avg_NBEADS", ??? ??? ??? ???Detection="Detection", ??? ??? ??? ???se.exprs="BEAD_STDEV") rather than what you currently have. 2. If I've counted correctly, it looks as if you have 6 lines of header information rather that 7. 3. Your sampleSheet is likely to cause problems - it looks like you are specifying the file which contains probe information rather than a file listing sample information about what was hybridised to each array. Best wishes, Matt <zoe.vanhavre at="" student.griffith.edu.au=""> wrote: > Hi, > I want trying to do? background correction to a Beastudio output file but I > can't read it into beadarray. > The sample file (.txt) has the following header: > > Illumina Inc. BeadStudio version 3.1.7 > > > Normalization = none > > > Array Content = HumanRef-8_V2_0_R0_11223162_A.bgx.xml > > > Error Model = none > > > DateTime = 24/09/2007 3:01 PM > > > Local Settings = en-AU > > > ? > > ProbeID??? TargetID ...etc > > > > The R code used and error message: > > > > PD.bstudiofile ='PD Vs Controls Only (n=70)_Sample_Probe_Profile_Nicko > edit.txt' > > sampleSheet = "HumanRef-8_V2_11223162_B.csv" > > > > PD<-readBeadSummaryData( > ??? dataFile=PD.bstudiofile, > ??? sampleSheet=sampleSheet, > ??? skip=7, > ??? ProbeID="ProbeID", > ??? columns = list(?? exprs = "AVG_Signal", > ??? ??? ??? ??? ??? ??? ??? ??? NoBeads = "Avg_NBEADS", > ??? ??? ??? ??? ??? ??? ??? ??? Detection="Detection", > ??? ??? ??? ??? ??? ??? ??? ??? BeadStDev="BEAD_STDEV")) > > Error in assayData(BSData)[[index]] = as.matrix(data[[i]]) : > ? attempt to select less than one element > > > > I've checked everything, tried different skip values, etc, with no luck! > > Please help me get this data loaded! sample information is > > > > sessionInfo() > > R version 2.7.1 (2008-06-23) > > i486-pc-linux-gnu > > > > attached base packages: > > [1] tools???? stats???? graphics? grDevices utils???? datasets? methods? > > [8] base???? > > > > other attached packages: > > ?[1] beadarray_1.8.0????? affy_1.18.2????????? preprocessCore_1.2.0 > > ?[4] affyio_1.8.0???????? geneplotter_1.18.0?? annotate_1.18.0???? > > ?[7] xtable_1.5-2???????? AnnotationDbi_1.2.2? RSQLite_0.6-9?????? > > [10] DBI_0.2-4??????????? lattice_0.17-10????? Biobase_2.0.1?????? > > [13] limma_2.14.5??????? > > > > thanks in advance for your advice > > Zoe van Havre > > > > Griffith University > > [[alternative HTML version deleted]]