User: jamie.gearing

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Posts by jamie.gearing

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Pre-ranked camera gene set testing with edgeR results
... Thanks very much Gordon! ...
written 11 days ago by jamie.gearing40
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5 follow
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Pre-ranked camera gene set testing with edgeR results
... Hello, I have inherited a table of differential expression results from edgeR (with logFC, logCPM, LR, PValue and FDR). Unfortunately, I do not have access to the original gene counts. I would like to perform some gene set testing using this data with the Broad MSigDB gene set collections. I was w ...
limma edger camera gene set testing camerapr written 11 days ago by jamie.gearing40 • updated 11 days ago by Gordon Smyth35k
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Comment: C: limma decideTests global method with multiple groups
... Thanks Aaron. I was leaning towards that particular choice, but it was very helpful to get another opinion. Yes, I shall just subset fit2 for the decideTests and then go from there. results.specific <- decideTests(fit2[,c("A.WT", "B.WT", "A.vs.B.WT", "A.KO", "B.KO", "A.vs.B.KO")], method = "glo ...
written 11 months ago by jamie.gearing40
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Comment: C: Random effects with limma's camera()
... Thanks Gordon. ...
written 11 months ago by jamie.gearing40
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limma decideTests global method with multiple groups
... Hello, I have an experiment with six groups: WT and KO cells that are untreated, treated with IFN A or IFN B. Here are some of the possible contrasts. cm <- makeContrasts( # Treatment effects A.WT = WT.A - WT.Un, B.WT = WT.B - WT.Un, A.KO = KO.A - KO.Un, B.KO = KO ...
limma decidetests written 11 months ago by jamie.gearing40 • updated 11 months ago by Aaron Lun21k
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Comment: C: Random effects with limma's camera()
... Can this now be addressed by using the recent pre-ranked cameraPR() function? i.e. run lmFit() with block and correlation, then eBayes() (or treat() if appropriate?) and use the t-statistics. ...
written 11 months ago by jamie.gearing40
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Comment: C: Limma filtering based on treatment group
... Very good. Thanks Steve. ...
written 16 months ago by jamie.gearing40
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Limma filtering based on treatment group
... Hello, I have a question about filtering lowly expressed probes (or genes) when using limma. For the example in section 17.4 of the limma user's guide, probes are called expressed if they exceed a cut-off in more than a given number of samples (equal to the size of the smallest treatment group): i ...
limma filtering written 16 months ago by jamie.gearing40 • updated 16 months ago by Steve Lianoglou12k
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Comment: C: chipenrich mm10 error
... Thanks very much for such a fast response! This package is just what I need, so I am very grateful. ...
written 18 months ago by jamie.gearing40
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chipenrich mm10 error
... I have encountered an error while trying to use the chipenrich package with the mm10 genome. Here is a small example: library(chipenrich) peaks <- data(peaks_E2F4, package = 'chipenrich.data') results <- chipenrich(head(peaks), out_name=NULL, genome = "mm10", genesets = c("GOBP", "GOCC", "GO ...
chipenrich written 18 months ago by jamie.gearing40 • updated 18 months ago by rcavalca120

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