Hello I have data from 5 Illumina mouse 6 beadarray slides. I have read in the bead level data using the beadarray package and used tapply to count the number of beads per probe. As an example, the output below is the summary and the top 10 counts for the first strip of the first array of my first slide. > summary(beadsPerProbe1[1,]) Min. 1st Qu. Median Mean 3rd Qu. Max. 7.00 30.00 35.00 35.71 41.00 3470.00 > s <- sort(beadsPerProbe1[1,], decreasing=TRUE) > s[1:10] [1] 3470 90 81 79 78 78 78 78 78 75 Unexpectedly (to me at least), there is one ProbeID with 3470 beads. There is a single ProbeID with a bead count > 3000 for each of the 60 strips. The probeID is different in every case. The data (e.g. BLData39A[[1]]$G) for the ProbeIDs with these high bead counts looks like sensible data. Does anyone know the meaning of this ProbeID with these high counts? I haven't included my code and sessionInfo() because I think this is a feature of the array rather than a programming error. Thanks for any help. Krys Dr Krystyna A Kelly (Krys) Department of Pathology University of Cambridge, Tennis Court Road, Cambridge CB2 1QP Tel: 01223 333331 and MRC Biostatistics Unit Institute of Public Health, Robinson Way, Cambridge CB2 0SR Tel: 01223 767408 Email: kak28 at cam.ac.uk

Hi Krys, Thanks for reporting this observation. I can't recall seeing beads with such high number of replicates, the most I get is around 100. My first thought is that these must be controls placed on the arrays by Illumina. Do you have an annotation file for the arrays? (should be called something like Mouse-6.csv in your case). This will list all the gene expression probes on the array. I would first suggest checking this file for the ProbeIDs you have found to have unusually high number of observations. Hope this helps, Mark On Fri, 2007-11-02 at 12:34 +0000, Krys Kelly wrote: > Hello > > I have data from 5 Illumina mouse 6 beadarray slides. I have read in the > bead level data using the beadarray package and used tapply to count the > number of beads per probe. > > As an example, the output below is the summary and the top 10 counts for the > first strip of the first array of my first slide. > > > > summary(beadsPerProbe1[1,]) > Min. 1st Qu. Median Mean 3rd Qu. Max. > 7.00 30.00 35.00 35.71 41.00 3470.00 > > > s <- sort(beadsPerProbe1[1,], decreasing=TRUE) > > > s[1:10] > [1] 3470 90 81 79 78 78 78 78 78 75 > > Unexpectedly (to me at least), there is one ProbeID with 3470 beads. > > There is a single ProbeID with a bead count > 3000 for each of the 60 > strips. The probeID is different in every case. The data (e.g. > BLData39A[[1]]$G) for the ProbeIDs with these high bead counts looks like > sensible data. > > Does anyone know the meaning of this ProbeID with these high counts? > > I haven't included my code and sessionInfo() because I think this is a > feature of the array rather than a programming error. > > Thanks for any help. > > Krys > > > > Dr Krystyna A Kelly (Krys) > > Department of Pathology > University of Cambridge, Tennis Court Road, Cambridge CB2 1QP > Tel: 01223 333331 > > and > > MRC Biostatistics Unit > Institute of Public Health, Robinson Way, Cambridge CB2 0SR > Tel: 01223 767408 > > Email: kak28 at cam.ac.uk > > _______________________________________________ > 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

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