User: Matt Ritchie

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Matt Ritchie460
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Posts by Matt Ritchie

<prev • 46 results • page 1 of 5 • next >
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Comment: C: SNPs data analysis
... Dear Mondher, I'd suggest you try using beadarraySNP. The beadarray package doesn't currently support BeadStudio output from Illumina's genotyping arrays. It will read in BeadStudio output from Illumina's expression arrays, and can handle raw bead-level data (text files and tiffs) for single-chann ...
written 11.0 years ago by Matt Ritchie460
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Illumina BeadChips and beadarray
... Dear Ina, It is my understanding that the intensities stored in the txt files have undergone 'local' background correction. This is a standard part of Illumina's image processing (i.e. not optional if you are going to use the intensities stored in the txt files by specifying useImages=FALSE). Thi ...
beadarray written 11.0 years ago by Matt Ritchie460
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Answer: A: Illumina BeadChips and beadarray
... Dear Ina, Thanks for the further detail. The intensities do look too low, especially when you use the tifs to reconstruct the bead-level intensities. If you put the tif and text files for these arrays online somewhere, I'll get someone to look into this in more detail. In the meantime, try analy ...
written 11.0 years ago by Matt Ritchie460
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Comment: C: Illumina BeadChips and beadarray
... Dear Ina, I can't see anything wrong with your commands (although you might find cor(exprs(BSData.Illumina.txt.013), method="pearson") is an easier way of getting the correlation between pairs of arrays). Are there any quality issues with this data set that could be driving this unusual result? ...
written 11.0 years ago by Matt Ritchie460
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Answer: A: Illumina BeadChips and beadarray
... Dear Ina, I'm not sure what the cause of this inconsistency could be. When I try the different background correction options available in readIllumina() on other data (I used the example data set at http://www.compbio.group.cam.ac.uk/Resources/illumina/SAMExample.zip - see below for the R code I r ...
written 11.0 years ago by Matt Ritchie460
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Answer: A: limits/thresholds for arrayWeights in the limma package
... Hi Radek, Arrays with weights less than 1 are less precise than average, while arrays with weights greater than 1 are more precise (the sum to zero constraint in the log-linear variance model enforces this). So in your example, the array which is assigned a weight of 4 is the most precise array in ...
written 11.0 years ago by Matt Ritchie460
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Answer: A: beadarray - can't load data
... Hi Zoe, There are a few things you could look at. 1. Check the columns argument in readBeadSummaryData(). I think it should be columns=list(exprs = "AVG_Signal", ??? ??? ??? ???NoBeads = "Avg_NBEADS", ??? ??? ??? ???Detection="Detection", ??? ??? ??? ???se.exprs="BEAD_STDEV") rather than wh ...
written 11.1 years ago by Matt Ritchie460
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Answer: A: Your thoughts on Limma Array Weights?
... Dear Paul, I have noticed cases where the results are 'better' (i.e. you get more extreme moderated t-statistics or log-odds) if you remove suspect arrays. In one recent example I recall, the experimenter eventually discovered that the genotype of a sample hybridised to one of their arrays was not ...
written 11.2 years ago by Matt Ritchie460
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Answer: A: subsetting an ExpressionSetIllumina object?
... Hi Jenny, Sorry to hear that subsetting isn¹t quite working as you would expect. Using the example data set available with the beadarray package I am able to subset probes/samples in the usual way without error. Do the following commands work ok for you? Best wishes, Matt > library(beadarray ...
written 11.2 years ago by Matt Ritchie460
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Answer: A: beadarray: how to apply imageplot() on BLData-outliers ?
... Hi Christian, There isn't an easy way to plot the intensities of the outlier beads only - I'm not sure that such a plot would be very informative. The function plotBeadLocations() may be worth a try though. This function plots the location of outliers, or other beads of interest on the array surfa ...
written 11.3 years ago by Matt Ritchie460

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