User: David Kipling

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David Kipling110
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Posts by David Kipling

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Pathway Information
... Hi Apologies to all for this being not strictly speaking BioC (although the back end does use some R/BioC functions to make heatmaps and the like)! Have a look at: http://www.madras.uwcm.ac.uk/ This is an Affy-focussed web-based environment where you can upload and review your data in a gene-cen ...
written 12.4 years ago by David Kipling110
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Comment: C: Analyzing mulitple tissues
... Dear Naomi, Gordon and Uri, If I might try to bring together Naomi's comments with those of Gordon and see if I have followed this correctly: Uri's original design is: Cardiac1, Cardiac2, Cardiac3 Skeletal1, Skeletal2 MSC That is, a 3x2x1 6-chip experiment. Naomi commented that with no replicat ...
written 12.5 years ago by David Kipling110
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Comment: C: Analyzing mulitple tissues
... Hi Naomi, I am glad you raised this issue of lack of replication. I fully take on board your point. Something is niggling me, however, so hopefully someone with a better stats background than me can help. What puzzles me is that limma will allow you to run experiments with no replication *and* w ...
written 12.5 years ago by David Kipling110
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Answer: A: Re: how to evaluate the arrays quality?
... Hi Also have a look at the simpleaffy package, which has some familiar but useful QC criteria presented in a coherent fashion. My own generic QC pipeline goes something like: require(affy) require(affyPLM) require(simpleaffy) # Input the cel files to an AffyBatch object data1 <- ReadAffy() ...
written 12.5 years ago by David Kipling110
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Use of RMA in increasingly-sized datasets
... Hi This is not a "how do I process 1000 chips with RMA" but rather something slightly different. We're starting to get projects coming thru our Affy core that involve 1000+ chips. Obviously we can use MAS5 to process the .cel files, and irrespective of what happens with subsequent chips in the p ...
cancer affy process written 12.5 years ago by David Kipling110 • updated 12.5 years ago by Darlene Goldstein230
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Rat 230 2.0 annotation package
... Hi Although I can find the rae230a and rae230b rat annotation metadata packages on the Bioconductor site, there doesn't seem to be one for the rat 230 2.0 chip (which is the combination of rae230a and rae230b). Is one available anywhere, and if not what would be the easiest way to make one (e.g. i ...
annotation rae230a rae230b written 12.5 years ago by David Kipling110 • updated 12.5 years ago by James W. MacDonald45k
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Answer: A: how to normalize by columns
... On 26 May 2005, at 07:12, diego huck wrote: > > Hello > > I am a beginner at bioconductor and R. I have a confussion about how > to do a normalization which consist of obtain the mean of a column, > and then substract the mean of the column to each value in the column. > x1 ...
written 12.5 years ago by David Kipling110
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AffyProbes and genome
... Hi The file Jim pointed you towards has a general location of the probeset (i.e. the region in which the 16 or thereabout probes are based). Somewhat more detail can be found in another Affymetrix file: http://www.affymetrix.com/Auth/analysis/downloads/psl/HG_U95Av2.link.p sl.zip This now gives ...
microarray alignment annotation cancer probe affy written 12.5 years ago by David Kipling110 • updated 12.5 years ago by Michael Janis20
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Answer: A: error opening corPlot.R
... Hi I think Swati is trying to source the corPlot.R file so that he gets access to the corplot() function within it. Just using ... file.choose() ... doesn't achieve this, but rather returns the full path to the corPlot.R file. If he wants to both find the file *and* source it to get the corplo ...
written 12.5 years ago by David Kipling110
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Answer: A: error opening corPlot.R
... > Sean Davis writes: >> You can see what the working directory is by: >> >> getwd() > > And you can see what is in the working directory with: > > dir() ..and (at least under RGui for Windows), you can get an interactive browser window to go on a file hunt: sourc ...
written 12.5 years ago by David Kipling110

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