Hi list, I have questions about beadarray package that I hope to get some answer or helpful hint from this list. 1. Where is the function DiffScore? I don't seem to be able to find this function although it was mentioned in the document "beadarray: An R package to Analyse Illumina BeadArrays"2006. 2. I want to make pair-wise comparisons between arrays. I have the bead level data available. A. Is background subtraction with background normalization is recommended? B. If here is no such function of DiffScore existing any more, should I do modified t-test on the summarized data on the beadlevel data? Thanks, Jeanie > sessionInfo() R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lumi_1.8.3 RSQLite_0.7-1 DBI_0.2-4 [4] preprocessCore_1.4.0 mgcv_1.4-1 affy_1.20.0 [7] beadarray_1.10.0 sma_0.5.15 hwriter_0.93 [10] geneplotter_1.20.0 annotate_1.20.1 xtable_1.5-4 [13] AnnotationDbi_1.4.2 lattice_0.17-17 Biobase_2.2.1 [16] limma_2.16.3 loaded via a namespace (and not attached): [1] KernSmooth_2.22-22 RColorBrewer_1.0-2 affyio_1.10.1 [4] grid_2.8.0 =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use\...{{dropped:13}}

Hi Jeanie, The DiffScore function is no longer part of beadarray as we do all of our analysis using the tools provided by the limma package .You should be able to do the tests you want with limma, the user guide that comes with the package is very helpful I would definitely recommend working with bead-level data if you have it. However, I don't find background normalization very helpful as it increases variability at lower intensities and creates negative intensities. If you do a log2 transformation (as one nearly always does for microarray analysis) after background normalization then you get a lot of missing values. The VST method in the lumi package is an alternative to log2 and can cope with negative intensities, however I've never really looked at whether doing VST with or without the background normalization makes a difference. Hope this helps, Mark On Wed, Apr 22, 2009 at 3:29 PM, Na, Jie <naj at="" ccf.org=""> wrote: > Hi list, > > I have questions about beadarray package that I hope to get some answer or > helpful hint from this list. > > 1. Where is the function DiffScore? I don't seem to be able to find this > function although it was mentioned in the document "beadarray: An R package > to Analyse Illumina BeadArrays"2006. > 2. I want to make pair-wise comparisons between arrays. ?I have the bead > level data available. > A. Is background subtraction with background normalization is recommended? > B. If here is no such function of DiffScore existing any more, should I do > modified t-test on the summarized data on the beadlevel data? > > Thanks, > > Jeanie > > > >> sessionInfo() > R version 2.8.0 (2008-10-20) > i386-apple-darwin8.11.1 > > locale: > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] tools ? ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods > [8] base > > other attached packages: > ?[1] lumi_1.8.3 ? ? ? ? ? RSQLite_0.7-1 ? ? ? ?DBI_0.2-4 > ?[4] preprocessCore_1.4.0 mgcv_1.4-1 ? ? ? ? ? affy_1.20.0 > ?[7] beadarray_1.10.0 ? ? sma_0.5.15 ? ? ? ? ? hwriter_0.93 > [10] geneplotter_1.20.0 ? annotate_1.20.1 ? ? ?xtable_1.5-4 > [13] AnnotationDbi_1.4.2 ?lattice_0.17-17 ? ? ?Biobase_2.2.1 > [16] limma_2.16.3 > > loaded via a namespace (and not attached): > [1] KernSmooth_2.22-22 RColorBrewer_1.0-2 affyio_1.10.1 > [4] grid_2.8.0 > > > =================================== > > P Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S. News & World Report (2008). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: ?This message is intended for use\...{{dropped:13}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >