User: Edwin Groot

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Edwin Groot230
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Posts by Edwin Groot

<prev • 23 results • page 1 of 3 • next >
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Answer: A: Affymetrix data
... On Fri, 13 Apr 2012 16:09:39 +0000 wrote: > > Dear all, > This question might sound very naive to most of you but I am new at > analyzing affymetrix array data using R/Bioconductor packages. > I have two cel files generated from HT430 Mouse genome. I have to > find differentially ...
written 7.5 years ago by Edwin Groot230
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Answer: A: Difference between LIMMA and Genespring
... Hello Ming, Hard to say something about your data without details on your preprocessing. The biggest difference in my experience is from the background subtraction and normalization steps. Check the normalization section of Agilent Feature Extraction software. This is what gives the green and red p ...
written 7.8 years ago by Edwin Groot230
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Predicted overlaps of 3 gene lists
... Hello all, I had an aha experience last night because of trying to count what would be in Venn diagrams. When calculating the expected overlaps of all pairwise combinations of 3 gene lists, I found out the the 3-way overlap is the combinatorial extension of the 2-way overlap formula. #Let Array Siz ...
written 8.0 years ago by Edwin Groot230
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Overlap of 3 gene lists and the Mantel-Haenszel test
... Hello all, For calculating the significance of the overlap of 2 gene lists I use either the Fisher exact test or the hypergeometric distribution. When I tried this on the overlap of 3 gene lists I have to make a 2x2x2 contingency table of what is IN or NOT in a list. Unfortunately the Fisher test ca ...
written 8.0 years ago by Edwin Groot230
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Limma: How to analyze 1- and 2- colour Agilent
... Hello all, I have a special Agilent 4x44 K microarray analysis problem. There are 4 replicates of 2-colour arrays comparing two cell types. I want to add to this 4 replicates each of 3 other cell types, but they are 1-colour hybridizations (array design is the same). How should I do the preprocessin ...
microarray limma written 8.9 years ago by Edwin Groot230
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Comment: C: multicore Vignette or HowTo??
... On Mon, 18 Oct 2010 09:34:31 -0700 Tim Triche wrote: > This may or may not help, but for truly independent calculations > (e.g. > reading and normalizing a pile of arrays) I find that writing a > function to > do the task end-to-end and then handing it off to > mclapply(list.of.k ...
written 9.0 years ago by Edwin Groot230
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Answer: A: New gage package: Generally Applicable Gene-set/Pathway Analysis
... On Tue, 19 Oct 2010 10:54:16 -0700 (PDT) Luo Weijun wrote: > Dear Bioconductor users, > I?d like to introduce my gage package newly released with Bioc 2.7. > Although the first version of gage package came out about two years > ago, this is its first release with Bioc. Please take a lo ...
written 9.0 years ago by Edwin Groot230
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Comment: C: multicore Vignette or HowTo??
... On Mon, 18 Oct 2010 09:39:22 -0700 Martin Morgan wrote: > On 10/18/2010 09:05 AM, Edwin Groot wrote: > > Hello all, > > I have difficulty getting the multicore package doing what it > promises. > > Does anybody have a benchmark that demonstrates something intensive > > ...
written 9.0 years ago by Edwin Groot230
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multicore Vignette or HowTo??
... Hello all, I have difficulty getting the multicore package doing what it promises. Does anybody have a benchmark that demonstrates something intensive with and without multicore assistance? I have a dual dual-core Xeon, and $ top tells me all R can squeeze from my Linux system is 25% us. Here is my ...
written 9.0 years ago by Edwin Groot230 • updated 9.0 years ago by Martin Morgan ♦♦ 23k
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Answer: A: Analysing expression with tiling arrays
... On Fri, 10 Sep 2010 09:30:11 +0200 January Weiner wrote: > Dear all, > > I have two tiling arrays of a bacterial genome. Unfortunately, I do > not have the original files (like the bpmap / cel files for Affy > tiling chips), just lists of spot intensities in two conditions for > ...
written 9.1 years ago by Edwin Groot230

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