User: andrew.birnberg

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Posts by andrew.birnberg

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Order of contrasts.fit call (before or after eBayes)
... Ok, so you're saying that the statistics reported by `topTable` after `contrasts.fit`, but before the second `eBayes` are based on incorrect variances? If so, what is `topTable` using to calculate its statistics? I had thought that only the gene-wise variances were updated by `eBayes` and that the c ...
written 5 months ago by andrew.birnberg20
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Comment: C: Order of contrasts.fit call (before or after eBayes)
... I'm not sure I'm clear on your suggestion. Is it necessary to call `eBayes` twice your workflow? What would be the effect in that case? ...
written 5 months ago by andrew.birnberg20
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Order of contrasts.fit call (before or after eBayes)
... Hello, I have run into a new issue (for me) in fitting a limma model. The model I am fitting includes a number of covariates/additional factors, such as ages and weights of individuals associated with a given "array", several random factors, such as race/ethnicity, region, and the factor defining m ...
limma written 5 months ago by andrew.birnberg20 • updated 5 months ago by Gordon Smyth37k
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Comment: C: Limma weights, non-specific interactions
... I agree, I would be making some very arbitrary choices here that could affect the analysis is unpredictable ways. I really like the idea of using a vector argument to lfc. I will play around with this. Removing the problematic interactors wouldn't work in our case since there may still be some biolo ...
written 11 months ago by andrew.birnberg20
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Comment: C: Limma weights, non-specific interactions
... Sorry for my delay in responding. The array is a functional protein array and interactions with the "prey" (proteins printed on the array) are detected by an antibody to the "bait" (what was put on the array). A non-specific interaction would be caused by "stickiness" of the prey. In general, we wou ...
written 11 months ago by andrew.birnberg20
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Limma weights, non-specific interactions
... Hi all, I am developing an analysis of protein microarray data and have found that limma performs very well in terms of identifying positive controls in the assay. Unfortunately, there are a large number of known, non-specific interactors that previous people have been identified in earlier experime ...
limma weight nonspecific filtering written 11 months ago by andrew.birnberg20 • updated 11 months ago by Gordon Smyth37k
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Comment: C: Difficulty extending ExpressionSet
... Thanks! I guess I had assumed that since no initialize method was defined for the subclass it would pass all its arguments unchanged to the parent class initialize method, like an implicit callNextMethod. I need to look more into SummarizedExperiment and how difficult it would be to interoperate wit ...
written 11 months ago by andrew.birnberg20
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Comment: C: Difficulty extending ExpressionSet
... I see what you're saying. After looking over the code for the RccSet class definition a bit, it looks like they had to create a new assayData environment instance out of a matrix before calling the ExpressionSet constructor and made a bunch of methods to cover their bases depending on the input. How ...
written 11 months ago by andrew.birnberg20
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Difficulty extending ExpressionSet
... Hello, This question was asked here previously around 7 years ago (https://support.bioconductor.org/p/36937/), however the answer seems to have either changed or the problem I'm facing is not the same. I am trying to write a class that extends ExpressionSet. I keep running into the following error: ...
biobase expressionset eset written 11 months ago by andrew.birnberg20 • updated 11 months ago by Martin Morgan ♦♦ 23k

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