User: Giovanni Coppola

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Posts by Giovanni Coppola

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LumiR
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written 12.2 years ago by Giovanni Coppola250 • updated 12.2 years ago by Pan Du1.2k
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Answer: A: problem with pamr.listgenes in pamr package
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written 12.4 years ago by Giovanni Coppola250
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Comment: C: limma user's guide example
... Hi Naomi and Jim, thanks for your replies. I agree that genes and p-values will stay the same. However, for this particular example, two possible approaches are presented, and - as they stand now - they are conflicting, yielding results with opposite signs. Best Giovanni On Oct 4, 2006, at 1:19 PM ...
written 13.0 years ago by Giovanni Coppola250
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limma user's guide example
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written 13.0 years ago by Giovanni Coppola250 • updated 13.0 years ago by Naomi Altman6.0k
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Answer: A: topTable gene list
... Hi Daphne, perhaps ?write.fit does what you want. Best Giovanni On Sep 13, 2006, at 7:13 AM, daphne mouzaki ((RI)) wrote: > hi, > > I have generated a list of significant genes for 3 time points > separately using the function > "decideTests"in Limma package.Using this function I ge ...
written 13.1 years ago by Giovanni Coppola250
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heatmap colors
... Hello everybody, some commercial packages (eg Genespring) include the expression level information (or some other kind of reliability index) in their heatmaps, changing the color brightness. Is there a way to do this using Bioconductor packages or R functions (heatmap.2, perhaps)? Many thanks in adv ...
written 13.2 years ago by Giovanni Coppola250
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Reading flag data from Agilent files
... Hello Frederic, you might be interested in this thread: http://article.gmane.org/gmane.science.biology.informatics.conductor/ 1822/ Best Giovanni On May 19, 2006, at 8:27 AM, Frederic Capel wrote: > Cher Monsieur, je viens demander un peu d'aide sur l'utilisation du > package Limma: j'esp? ...
limma written 13.4 years ago by Giovanni Coppola250
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biomaRt and wormbase: gene dataset
... Hello, I am trying to get human and mouse homologs from worm genes. I am querying wormbase using biomaRt. I get an error when trying to use the 'gene' dataset (example below). The other datasets work fine. Is there a way around this? Thanks Giovanni library(biomaRt) Loading required package: XML L ...
biomart written 13.4 years ago by Giovanni Coppola250
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Comment: C: getBM (biomaRt) sometimes returns NULL
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written 13.6 years ago by Giovanni Coppola250
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Comment: C: getBM (biomaRt) sometimes returns NULL
... Hello Wolfgang, I am actually getting a different error now... the wormids list is usually much longer. > wormids<-c("ZK666.6","Y41C4A. 11","T02G5.7.1","K08F4.7","A_12_P11025","ZC410.5b","C32H11.2","F54D11. 1" ) > getBM (attributes=c ("wormbase_gene","go_description"),filter="wormbase_ge ...
written 13.6 years ago by Giovanni Coppola250

Latest awards to Giovanni Coppola

Popular Question 12.2 years ago, created a question with more than 1,000 views. For limma and p-values

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