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]]
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]]
