User: Mark Cowley

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Mark Cowley400
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Posts by Mark Cowley

<prev • 38 results • page 1 of 4 • next >
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Answer: A: Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "det
... Hi Bill, My goal for lumidat was to recapitulate the behaviour of GenomeStudio, for better or for worse. As noted by Gordon, and as you can see below in the code, the actual behaviour of GS contradicted the software manual. I like Gordon's idea of detecting & converting them to proper p-values. ...
written 2.2 years ago by Mark Cowley400 • updated 2.2 years ago by Gordon Smyth32k
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Comment: C: xps - creating ROOT scheme fi les
... Hi Benilton, i'm using oligo in a processing pipeline which runs out of RAM with >15 exon arrays, so I was considering switching to xps. However, i'm intrigued by your comment re 'if you think you have enough RAM for the expression matrix'. Are you implying that you can use oligo on quite large n ...
written 7.4 years ago by Mark Cowley400
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Comment: C: Repeat Measurement with Limma Fw: limma matrix desgin question?
... hi, you could still treat each strain x time x treatment combo as a separate group, ie 10 groups, and then use contrasts to compute the average 0_t1 effect over the 3 mice, eg: # i've reformatted you contrast matrix creation line -- i don't know why you've duplicated your contrasts here contrast.mat ...
written 7.5 years ago by Mark Cowley400
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Answer: A: Repeat Measurement with Limma Fw: limma matrix desgin question?
... hi Xiaokuan, i'd be treating the technical replicates as the block, and strain, day and treatment as the biological effects of interest block <- rep(1:10, each=3) that way limma has triple the number of arrays to use in its variance estimation you have a few options for your design matrix, such ...
written 7.5 years ago by Mark Cowley400
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Answer: A: Correlation analysis of replicates
... Hi Kai, i'm not sure about your first question, but... re the correlation coefficient, take a look at the GeneSelector package. In their original paper, they called the correlation an OrderScore if I recall correctly. cheers, Mark ----------------------------------------------------- Mark Cowley, P ...
written 8.0 years ago by Mark Cowley400
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Comment: C: Affymetrix genechip miRNA array analysis
... Hi, you can download the CDF from Affymetrix, so you *should* be able to run a simple affy and limma analysis; however there are lots of different species on this chip, so you may want to subset probes to the relevant ones for your species prior to the limma analysis (my version of the affy miRNAQCt ...
written 8.1 years ago by Mark Cowley400
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From pilot to a large study
... Dear list, Rather than reinventing the wheel, I hope someone in the community can point me in the right direction. In a pilot study, we have looked at a single xenograft over time (0,8,24,48 hours) with or without drug treatment (7 groups). Using Illumina WG6 arrays, with biological quadruplicates ...
written 8.2 years ago by Mark Cowley400
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Comment: C: Compiling graph on solaris
... Dear Herv?, Thanks for looking into this for me, i really appreciate it. www.bioconductor.org seems to be down at the moment, but i'll report back if i have success I'm using GNU ld and gcc $ which ld /opt/csw/bin/ld $ ld -v GNU ld version 2.17 $ gcc -v Reading specs from /usr/local/lib/gcc/i386-p ...
written 8.2 years ago by Mark Cowley400
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Compiling graph on solaris
... Dear list, I just upgraded to R 2.9.2, on solaris 10, and stumbled across a problem with graph. The package installed with 1 warning, but no errors. When I load it, I get the following error: > library(graph) Error in library.dynam(lib, package, package.lib) : shared library 'BioC_graph' not ...
graph written 8.2 years ago by Mark Cowley400 • updated 8.2 years ago by Aric Gregson50
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Comment: C: One-color spotted microarrays analysis
... Hi Pier-Luc, What sort of within array normalisation are you trying to perform? ie what issues have you spotted in your data that you think need removing? There are no print-tip's as such on an agilent array since they're printed by fancy ink jet printers. You can't do lowess, unless you make a 'vi ...
written 8.5 years ago by Mark Cowley400

Latest awards to Mark Cowley

Scholar 2.2 years ago, created an answer that has been accepted. For A: Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "det
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "det

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