User: Scott Ochsner

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Scott Ochsner300
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Posts by Scott Ochsner

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Help with getBM using EST ids from zebrafish
... Dear list, I am trying to retrieve zfin annotation for each of my 6000+ zebrafish EST ids using biomaRt. As an example of the EST ids I've included the output from NCBI's EST search for CO349769. 1. DR_AOV_FL01_G08 adult ovary full-length (TLL) Danio rerio cDNA, mRNA sequence gi|49431086|gb|CO349 ...
annotation danio rerio biomart written 10.5 years ago by Scott Ochsner300 • updated 10.5 years ago by Wolfgang Huber13k
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In need of platform clarification for 2-color SMD arrays
... Dear BioC, I've used the GEOquery package as below to upload GSE7585. This created a list of two ExpressionSets as predicted, one for each platform. > gse<-getGEO("GSE7585",GSEMatrix=TRUE) > names(gse) [1] "GSE7585-GPL3417_series_matrix.txt.gz" "GSE7585-GPL5118_series_matrix.txt.gz" > ...
geoquery written 10.5 years ago by Scott Ochsner300
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Answer: A: Generating random gene lists: does sample/resample generate random sets
... Thomas, Sean, I see your reasoning and will leave the curated list of genes in the universe prior to random list generation. However, what about the following scenario? Lets say the genes are left in, 1000 random gene lists are generated, and each of these are tested for their classification per ...
written 10.7 years ago by Scott Ochsner300
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Generating random gene lists: does sample/resample generate random sets
... Thomas, I wanted to asses the performance of random gene lists which do not have any overlap with myCuratedList hence the step to remove them from the universe of possible genes prior to random gene selection. If I leave the curated genes in, random lists could potentially be produced with signifi ...
classification written 10.7 years ago by Scott Ochsner300
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Answer: A: Generating random gene lists: does sample/resample generate random sets
... Sorry, Below is my sessionInfo() > sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] spl ...
written 10.7 years ago by Scott Ochsner300
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Generating random gene lists: does sample/resample generate random sets
... Dear BioC, I would like feedback as to the appropriateness of the following procedure to produce a set of 1000 random gene lists, each list of length 2000. The idea is to use the set of random gene lists to assess how often random gene lists of size x can reproduce or improve the classification pe ...
classification written 10.7 years ago by Scott Ochsner300 • updated 10.7 years ago by Thomas Hampton740
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Comment: C: Variations of plotting symbols
... Kamila, Thanks, This is exactly what I needed. I failed to dig deep enough into the points documentation. Scott -----Original Message----- From: Kamila Naxerova [mailto:knaxerova@chip.org] Sent: Thursday, September 04, 2008 7:30 PM To: Ochsner, Scott A Cc: bioconductor at stat.math.ethz.ch Subj ...
written 10.7 years ago by Scott Ochsner300
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Variations of plotting symbols
... Dear BioC, I have five microarray datasets each with two levels. I'm plotting a PCA figure and would like to avoid using color as page charges for color in the journal I wish to submit are expensive. Is there a way to turn the solid triangle symbol (pch=17) 180 degrees? This would add enable me t ...
microarray go written 10.7 years ago by Scott Ochsner300 • updated 10.7 years ago by Kamila Naxerova40
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Assess inter-study consistency
... Dear BioC, I would like to use simple correlation to assess the consistency between a seven independent expression array datasets. All datasets are on the same platform, hgu133a. In the materials and methods section from http://cancerres.aacrjournals.org/cgi/content/full/67/21/10296#top they stat ...
go hgu133a probe written 10.7 years ago by Scott Ochsner300 • updated 10.7 years ago by Thomas Hampton740
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Following meta-analysis, how to address type 2 error?
... Dear BioC, I've been using a weighted Stouffer method to combing p-values (one- tailed) derived from multiple microarray experiments performed in independent labs. Each experiment roughly address the same null hypothesis: addition of receptor ligand for 24h has no effect on gene expression. I ha ...
microarray written 10.9 years ago by Scott Ochsner300

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