User: Assaf Oron

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Assaf Oron40
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10 years, 11 months ago
Joined:
11 years, 2 months ago
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a****@fhcrc.org

Posts by Assaf Oron

<prev • 4 results • page 1 of 1 • next >
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St. Jude's Ross Et al. (2003) dataset in ExpressionSet form?
... Hi all, Does anyone have lying around the St. Jude dataset used in Ross et al. 2003, "Classification of Pediatric ALL by Gene Expression Profile", in a form that has already undergone summarization, normalization and pre-processing to an ExpressionSet, or even just a pre-processed feature vs. sampl ...
normalization written 10.9 years ago by Assaf Oron40
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Gene Pre-filtering: My Two Shekels
... Hi all, Allow me to add my perspective as a relative newcomer into this field. At first I too was alarmed by the apparent violation of statistical orthodoxy involved in pre-filtering. But after witnessing how well this works on real data, my opinion has changed. I feel that either the statisticia ...
microarray written 11.0 years ago by Assaf Oron40 • updated 11.0 years ago by Talloen, Willem [PRDBE]40
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Finding genes with significant linear regression, or trend
... Daniel hi, You can also try the function "lmPerGene" from the new package GSEAlm. This function allows for continuous covariates without recoding them as factors. The function returns an object, say "mylm". To get the t-statistics, divide "mylm$coefficients" by "sqrt(mylm$coef.var)". Note that the ...
gsealm written 11.1 years ago by Assaf Oron40
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GOstats gene set size selection
... Alex hi, I'm not sure whether you can directly prevent the hyperGTest function from testing small gene-sets. It tests all gene-sets as a default. However, you can certainly filter the list of significant gene-sets by set size. The summary() function for the test output has a "categorySize" argume ...
written 11.2 years ago by Assaf Oron40

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