User: Massimo Pinto

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Massimo Pinto390
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Posts by Massimo Pinto

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Answer: A: limma: writing down the matrix in an almost (?) factorial design experiment
... I thought I should add here how the design matrix was created. Probably, if I understand the language correctly, this is a mixed factorial/nested design with three two-level factors: Dose <- factor(targets$Dose, levels=c("Cn", "1Gy")) # It's very important that you define the levels now, with th ...
written 9.8 years ago by Massimo Pinto390
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limma: writing down the matrix in an almost (?) factorial design experiment
... Dear all, I am writing in relation to some doubts that I have on the implementation of a design matrix in a factorial design experiment. I have tried to follow, religiously, the recommendations as at paragraph 23.10 of the R&Bioconductor monography, but have come up with several afterthoughts. ...
microarray dose written 9.8 years ago by Massimo Pinto390
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on the meaning and value of $stdev.unscaled in a limma's lmFitted MArrayLM object
... Greetings all, I am writing to enquire about the meaning of some elements that are provided in an limma::MArray-LM object resulting from a call to limma::lmFit(); To avoid a verbose output, I tried to minimize the number of genes to be fitted, by selecting just two genes from my expression set: & ...
go hgug4112a probe written 10.0 years ago by Massimo Pinto390
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Comment: C: End of the line of GOstats: making sense of the hypergeometric test results now
... Thank you to both. @Robert: I have run the hyperTest both conditionally and not and noticed that the effect is rather substantial: the list of significantly implicated nodes does get shorter when conditional=TRUE. @James: how do you tell a more general node from a less general? Do you merely count ...
written 10.1 years ago by Massimo Pinto390
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End of the line of GOstats: making sense of the hypergeometric test results now
... Greetings all, Having first searched the GMane archives, I suppose the following question is appropriate. After selecting my 'entrezUniverse', I have run an hypergeometric test, as implemented in functions provided in GOstats, and thus obtained a readable, hyperlinked report containing a list of th ...
go written 10.1 years ago by Massimo Pinto390 • updated 10.1 years ago by James W. MacDonald52k
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Comment: C: comparing two or more limma::topTables - in search of a graphical tool
... Dear James, thank you for your kind and prompt reply. I had always used vennDiagrams() on the outcome of limma::decideTests(), which, upon reading the ?vennDiagram help, I gather is only one of two options, the other being what you are pointing at. I have tried to play with vennCounts() to feed Ve ...
written 10.1 years ago by Massimo Pinto390
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comparing two or more limma::topTables - in search of a graphical tool
... Greetings all, in an experiment which I have analyzed using a factorial design, I have reached a point where I have produced a number of fits to my data with several contrasts and I am interested in making some comparisons between the two or more lists of differentially expressed genes. One tool, a ...
written 10.1 years ago by Massimo Pinto390 • updated 10.1 years ago by James W. MacDonald52k
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error while using genefilter's nsFilter: could not find function "hgug4112a.db_dbconn"
... That indeed solved the problem. > annotation(esetPROC) <- "hgug4112a" # Very important. Must remove that .db from the name of the annotation package. > esetGSEA <- nsFilter(esetPROC, require.entrez=TRUE, require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.cutoff=0.3) # cutoff at ...
annotation hgug4112a written 10.1 years ago by Massimo Pinto390
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error while using genefilter's nsFilter: could not find function "hgug4112a.db_dbconn"
... Greetings all, I have finally come across to genefilter's nsFIlter(); it looks like it's going to do quite a lot for me in just one call. I called it as follows: > esetGSEA <- nsFilter(esetPROC, require.entrez=TRUE, require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.cutoff=0.5) Err ...
hgug4112a written 10.1 years ago by Massimo Pinto390 • updated 10.1 years ago by rgentleman5.5k
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Comment: C: Agi4x44PreProcess 1.4.0 question: use of genes.rpt.agi() and Gene Sets
... On Tue, Oct 27, 2009 at 4:54 PM, Francois Pepin wrote: >> Are there any functions written to address each of these topics? > >> 1) choosing the probe with the largest experimental variation (or with >> the maximum average) > > ?genefilter::findLargest should point you in ...
written 10.1 years ago by Massimo Pinto390

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