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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
UCLA
phone: +1-310-2060133
email: yhasin at mednet.ucla.edu
-- output of sessionInfo():
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[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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