beadarray package - analysis of bead summary level data
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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 -- Sent via the guest posting facility at bioconductor.org.
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wenhuo hu ▴ 200
@wenhuo-hu-5208
Last seen 3.6 years ago
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Hi, I have no experience on this package. A wide guess here, is it possible the qcfile and datafile have different rows after read into R? Say, repeat rows were delete in qcfile but not datafile. Wenhuo On May 28, 2012 9:10 PM, "Yehudit Hasin [guest]" <guest@bioconductor.org> wrote: > > 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@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 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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