Thank you for you comments, Mark and Cei. Just another quick question: the number of beads per probe that are detected in the different arrays of the 8-array slide is slightly lower in the the array with the white streaks compared with a "normal" array in the same slide (median:36 vs. 41; min: 9 vs. 13). Could this potentially bias the analysis (I'm using lumi) in such a way that I should ask Illumina to replace the array? And, if so, is this a common enough problem with Illumina to raise concerns about the reliability/ reproducibility of this platform? Thanks again, Luis. On Mar 5, 2009, at 5:28 AM, Mark Dunning wrote: > Hi Luis, > > The white streaks you see on the imageplots are because of missing > data on the array. This occurs when the Illumina scanner is unable to > decode the identity of beads on the array. Information about these > undecoded beads is not reported in the output that comes out from the > scanner and therefore we cannot use them in any analysis, including > BASH. > > The white streaks would not show up in the BeadStudio images or the > TIFF images generated by the scanner as these are just the raw pixel > intensities and do not take bead identity into account. > > Hope this helps > > Regards, > > Mark > > On Thu, Mar 5, 2009 at 2:13 AM, Luis Fernando Menezes <lmenezes at="" jhmi.edu=""> > wrote: >> Hello. >> >> I have been using beadarray (v. 1.10.0) to analyze some Illumina >> mouse >> ref8v2 arrays. >> When I import the images and expression data using readIllumina() >> and plot >> them using imageplot() [either before or after background >> subtraction], I >> get an unusual pattern that would suggest some sort of artifact in >> the >> array, with "white streaks" across it. >> When I questioned the core who had done the microarray experiment, >> they said >> the BeadStudio image did not show any of the odd patterns. >> Using outlierPlot() or BASH, some areas were flagged for masking, >> but they >> did not match the "white streak areas" (I assume that is because the >> outliers would in general have increased expression levels, as >> opposed to >> the white areas with almost no signal). >> >> My questions are: >> 1) is there any reason why the images generated by BeadStudio and >> beadarray >> should be different? >> 2) why are the streaks with almost no signal not flagged as regions >> that >> should be masked? >> 3) should I be concerned about these low signal streaks? >> >> Thank you. Best regards, >> >> Luis. >> >>> sessionInfo() >> R version 2.8.0 Patched (2008-10-22 r46776) >> i386-apple-darwin9.5.0 >> >> 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 >> base >> >> other attached packages: >> [1] beadarray_1.10.0 sma_0.5.15 hwriter_0.93 >> geneplotter_1.20.0 annotate_1.20.0 xtable_1.5-4 >> AnnotationDbi_1.4.1 >> [8] lattice_0.17-15 Biobase_2.2.0 limma_2.16.2 >> >> loaded via a namespace (and not attached): >> [1] DBI_0.2-4 KernSmooth_2.22-22 RColorBrewer_1.0-2 >> RSQLite_0.7-0 >> grid_2.8.0 >> >> _______________________________________________ >> 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 >>