User: Mark Dunning

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Mark Dunning320
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Posts by Mark Dunning

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Comment: C: How to create a GO2gene object for topGO?
... Hello all, I have been looking at the mdqc package for automatic quality assessment of a large set of Affy SNP 6.0 data. I have already generated a set of QC stats using Affy's own software and they exclude outlier arrays using a fixed cut-off of the contrast QC scores (basically a measure of how s ...
written 10.8 years ago by Mark Dunning320
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Answer: A: Beadarray and illumina methylation arrays
... Hi Katrina, I only have limited experience with methylation data, but hopefully I might be able to give you a few pointers. -The error with readIllumina is quite hard to diagnose without seeing the example. I haven't seen any data from this type of Methylation array. What do the first few lines of ...
written 10.8 years ago by Mark Dunning320
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Comment: C: Filtering in Beadarray package
... Hi Allen, For filtering Illumina data, most people seem to use the 'detection pval' column and remove genes which are not present on *any* array in the experiment. However, I agree with Sean's comment that a gene being expressed all the time is not enough to qualify it as being "interesting" and fi ...
written 11.2 years ago by Mark Dunning320
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Answer: A: lumi: target ids versus probe ids?
... Hi Michal, I would definitely recommend working with the probe-level data rather than the gene-level data. I have seen many examples of genes with multiple probes where the results from different probes can look completely different: one probe can be unexpressed all the time, whereas the other can ...
written 11.3 years ago by Mark Dunning320
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Multiple colours in GenomeGraphs?
... Hi all, I have just started using the GenomeGraphs package, which I think is a really good piece of software :) I am using the package to plot expression values across a genomic region. However, it seems to plot all points on the same "track" in the same colour? I was wondering if it is possible t ...
genomegraphs written 11.3 years ago by Mark Dunning320 • updated 11.3 years ago by James Bullard70
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Answer: A: beadarray_1.7.6. problem/error with readBeadSummaryData()
... Hi Christian, This script was a bit outdated I'm afraid. The package was recently changed so that it would use the ProbeID column in the input files to give a unique row name in the resulting ExpressionSet. Unfortunately, the file provided with the package did not have this column, hence R gives an ...
written 11.4 years ago by Mark Dunning320
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Answer: A: Analysis of Illlumina methylation array data using beadarray
... Hello Ed, I think the best option would be work from the raw (bead level) data when trying to understand more about the technology. To do this, the settings.xml file will indeed need to be modified prior to scanning. I can give you more details about that if you're not sure how to do it. The funct ...
written 11.8 years ago by Mark Dunning320
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Answer: A: Using beadarray for bead level data, what is the ProbeID with 1000's of beads?
... 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 somethin ...
written 11.8 years ago by Mark Dunning320
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Answer: A: beadarray - combing
... Hi Krys, Sorry, it seems that the manual page for createBeadSummaryData is either out of date or contains a typo. The function we use to join summarised data is actually called combine so you would use BSData = combine(BSData39ABC, BSData39DEF) to get the required result. Hope this helps and th ...
written 12.0 years ago by Mark Dunning320
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Answer: A: ControlID Qcinfo slot in Illumina beadarray summary data?
... Hi, Unfortunately, this is a bug with version 1.4.0 of beadarray. It will try and read the TargetID column from the quality control file, but there is no slot in the BSData object to put this information in. And this is the message that beadarray gives. Anyways, the BSData object should still be v ...
written 12.0 years ago by Mark Dunning320

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