[BioC] beadarray package - analysis of bead summary level data

Yehudit Hasin [guest] guest at bioconductor.org
Tue May 29 03:09:41 CEST 2012

Hi all

My name is Yehudit, I am from UCLA. I am new to this forum, and to microarray analysis - hope someone could help:) 
Goal: trying to analyze Illumina HT v4 arrays, but I have access only to the bead summary data, and was hoping to use "beadarray" package for analysis (should I use something else?). 
The tutorial on sample data worked just fine, so I moved to my data. I used GenomeStudio Gene expression to create 2 files:
dataFile -data not normalized, no background subtraction. File includes TargetID, ProbeID + average signal, number of beads, beads std error and detection p value for each array. 
qcFile - control probes with the same info. 
These were read into BSData:

> dataFile="5donors_nonorm_nobgd.txt"
> qcFile="5donors_nonorm_nobgd_cotrolprobe.txt"
> BSData = readBeadSummaryData (dataFile = dataFile, qcFile = qcFile,controlID = "ProbeID", sep="\t", skip = 0, qc.skip = 0, qc.columns = list(exprs = "AVG_Signal", Detection = "Detection Pval"))
Warning message:
In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns,  :
  controlIDs non-unique: 4 repeated entries have been removed.

I ignored the warning message (as it seemed to remove the duplicates anyway), and tried to use channel to create another ExpressionSetIllumina object for plotting (as in tutorial). Here I got stuck:
> channelNames(BSData)
[1] "G"

> BSData.ul<-channel(BSData,"G")
Error in assayDataNew(exprs = exprs(object)[, selArray], se.exprs = se.exprs(object)[,  : 
  'AssayData' elements with different rowNames
In addition: Warning messages:
1: In eltRowNames == rownames(assayData[[elt]]) :
  longer object length is not a multiple of shorter object length
2: In eltRowNames == rownames(assayData[[elt]]) :
  longer object length is not a multiple of shorter object length

Another question that I can't seem to find the answer to is how to create a second channel with log transformed data in the BSData?

I am running Rstudio 0.96.122 with R 2.15.
Thank you in advance, any help would be greatly appreciated!

Yehudit Hasin, PhD
David Geffen School of Medicine
Dept. of Cardiology, Gonda 6524
phone:	+1-310-2060133
email: 	yhasin at mednet.ucla.edu

 -- output of sessionInfo(): 

R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] C/en_US.UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] beadarray_2.6.0    ggplot2_0.9.1      Biobase_2.16.0     BiocGenerics_0.2.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.18.1 BeadDataPackR_1.8.0  DBI_0.2-5           
 [4] IRanges_1.14.3       MASS_7.3-18          RColorBrewer_1.0-5  
 [7] RSQLite_0.11.1       colorspace_1.1-1     dichromat_1.2-4     
[10] digest_0.5.2         grid_2.15.0          labeling_0.1        
[13] limma_3.12.0         memoise_0.1          munsell_0.3         
[16] plyr_1.7.1           proto_0.3-9.2        reshape2_1.2.1      
[19] scales_0.2.1         stats4_2.15.0        stringr_0.6         
[22] tools_2.15.0   

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