User: Paolo Innocenti

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Posts by Paolo Innocenti

<prev • 32 results • page 1 of 4 • next >
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Answer: A: Problem with lmfit
... Hi, I can reproduce the error, which seems to be caused by your expressionset having only one feature. If you try with 2 lines, it works: library(Biobase) library(limma) design <- matrix(c(1,0),ncol=2,nrow=5,byrow=T) design <- rbind(design,c(0,1),c(0,1)) colnames(design) <- c("HEALTHY","D ...
written 8.3 years ago by Paolo Innocenti320
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Answer: A: identical output plots for NUSE AND RLE
... Try with: # RLE Mbox(plm, main="RLE") # # NUSE boxplot(plm, main="NUSE") more info at section 3.5.1 (pag.45) of "Bioinformatics and computational biology solutions using R and BioConductor", Gentleman R. et al. (2004). best, paolo On 06/22/2010 03:32 PM, Richard Friedman wrote: > Dear List, ...
written 8.4 years ago by Paolo Innocenti320
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Limma and p-adjust: 'global' on non-orthogonal contrasts?
... Dear Gordon and list, I have a question about p-value adjustment for multiple testing across contrasts. Let's say we have three groups, as in the Limma user guide, section 8.6, and this contrasts are closely related one another, so we want to apply method="global" to decideTests(). The code in se ...
limma written 8.4 years ago by Paolo Innocenti320
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Model simplification on microarray data
... Dear list, I am working with Affymetrix GeneChip gene expression arrays. I am fitting to every transcript a mixed model (using lme4) that looks like this: lmer(Y ~ female.type*male.type+(1|female.pop)+(1|male.pop)) where Y is the transcript signal. When looking at the results, I realized that man ...
written 8.6 years ago by Paolo Innocenti320
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RMA (model II) regression with lmFit
... Dear list, does anyone know if it is possible to fit a RMA (Reduced Major Axis, or model II) regression in limma? The difference should basically be that it assumes error on the x as well, instead of just on the response variable. In other words, instead of minimizing the the residual on the verti ...
regression written 9.4 years ago by Paolo Innocenti320
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Problem with Hopach: "Error in dmat[ord, ]"
... Dear Vincent and list, hopefully I managed to provide a non-working example. It looks like the lme4 (the lme4-required package Matrix in particular) causes some incompatibilities: library(lme4) require(hopach) data(golub) vars <- apply(golub, 1, var) subset <- vars > quantile(vars, (nrow( ...
drosophila2 hopach written 9.4 years ago by Paolo Innocenti320
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Random effects and variance components (was: Yet another nested design in limma)
... Dear Gordon and list, thanks for the previous help, it was indeed helpful. Nonetheless, even after some strolling (and independent trials-and-errors), I am still stuck on this issue: we came to the conclusion that the simplest good model for our affy experiment is the following: design <- mode ...
affy limma siggenes factdesign maanova written 9.5 years ago by Paolo Innocenti320 • updated 9.5 years ago by James W. MacDonald48k
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Comment: C: Problem with Hopach: "Error in dmat[ord, ]"
... Hi Vincent, thanks for the help, I emptied the R workspace and tried again. Both the example and my own code work now. Something in the workspace was probably conflicting with it. No idea what. I am happy with that at the moment... Thanks, paolo > require(hopach) Loading required package: ho ...
written 9.5 years ago by Paolo Innocenti320
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Problem with Hopach: "Error in dmat[ord, ]"
... Hi all, I'm experiencing this problem with hopach package. The following code runs just fine in a fresh session, but gives an error (see below) in my working directory: > require(hopach) > data(golub) > vars <- apply(golub, 1, var) > subset <- vars > quantile(vars, (nrow(g ...
drosophila2 hopach written 9.5 years ago by Paolo Innocenti320 • updated 9.5 years ago by Vincent J. Carey, Jr.6.2k
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Category: testing for non-random chromosomal distribution of DE genes
... Hi all, I wanted to test for chromosomal region enriched for my list of DE genes. I tried with the ChrMapHyperGParams but it looks like that just Human and mice are supported (see below). I am really interested in this approach, and would like to know if it would be difficult to implement such sup ...
go organism drosophila2 written 9.5 years ago by Paolo Innocenti320 • updated 9.5 years ago by Marc Carlson7.2k

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Popular Question 8.3 years ago, created a question with more than 1,000 views. For Random effects and variance components (was: Yet another nested design in limma)

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