User: Marcelo Luiz de Laia

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Posts by Marcelo Luiz de Laia

<prev • 77 results • page 2 of 8 • next >
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Comment: C: [Limma] M value in contrast test
... James W. MacDonald escreveu: >Does that help? > > > Dear Dr. James W. MacDonald, Your replay is very helpful! I did these analysis for a colleague and her need to known what M means in that situation. You save my life! I thank you very much! Marcelo ...
written 14.1 years ago by Marcelo Luiz de Laia770
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[Limma] M value in contrast test
... Hi limma Users, I did a contrast in our analisis like this: (mutant treated-mutant control)-(wildtype treated-wildtype control) We are interested in to known what "M" value means in this situation? In limma users guide there are two interpretation for "M" value: fold change or intensities. Than ...
limma written 14.1 years ago by Marcelo Luiz de Laia770 • updated 14.1 years ago by James W. MacDonald52k
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[OT] Help to creating a function to automate the plotProfile function in timecourse
... Hi All, I would like to save the firts 500 (1 to 500th) graphs made by plotProfile function in timecourse package in a batch command. The function is: - for gene 1: plotProfile(out2,type="b",gnames=gnames,pch=c("A","B","C"),xlab="Tempo ",ranking=1 - for gene 2: plotProfile(out2,type="b",gnames=gn ...
timecourse written 14.2 years ago by Marcelo Luiz de Laia770 • updated 14.2 years ago by Ido M. Tamir320
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Cannot find xml2-config
... Hi All, I am try to update my Bioconductor to new release (thank you, Seth, for the best release and for increase the number of packages. Congratulations to the whole BioC team for the new release!) and try to install a few new packages. But, I got this error: checking for xml2-config... no Canno ...
written 14.2 years ago by Marcelo Luiz de Laia770 • updated 14.2 years ago by Seth Falcon7.4k
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[OFF TOPIC] Script/Software to prediction of bacterium promoter element
... Dear Sir/Maddam, Please, can you suggest me a script or software to predict promoter region in bacterium genes? Thank you very much Marcelo Luiz de Laia Ph.D Student http://www.unesp.br/eng ...
written 14.2 years ago by Marcelo Luiz de Laia770
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heatmap and hcluster from limma out put object
... Hi Bioconductor's Users, I found in the list archives a step-by-step for to do a heatmap with a hclust. It is in: http://files.protsuggest.org/biocond/html/1127.html ///I tested it and I modifield it to my code, like this: [1]dist.x <- dist(exprs(todos.norm),method="euclidean",diag=TRUE) cl ...
pathways limma written 14.3 years ago by Marcelo Luiz de Laia770
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M value in topTable and Fold Change
... Dear limma users and all bioconductor's users, I have four questions about the subject. I analyzed our data in the following way: library(limma) library(affy) todos <- read.matrix("todos.txt",sep="\t") todos <- log2(todos) todos.norm <- normalize.quantiles(todos) design <- model.matri ...
go limma written 14.5 years ago by Marcelo Luiz de Laia770
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Error installing genefilter
... Hi, When I try to install package genefilter, I receive this error message: root@lbmsala4b:/home/kurumin/Temp# R CMD INSTALL -l /usr/lib/R/library genefilter_1.5.0.tar.gz * Installing *source* package 'genefilter' ... ** libs gcc -I/usr/lib/R/include -fPIC -g -O2 -c genedist.c -o genedist.o g ...
annotate genefilter affy vsn written 14.6 years ago by Marcelo Luiz de Laia770 • updated 14.6 years ago by Wolfgang Huber13k
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quality data check
... Dear All, We work with cDNA in nylon membranes. We use bioconductor to analyze our data, basically, the packages limma, affy and vsn. The normalizations are made using normalize.quantiles from affy package. However, to verify the quality of the data from this platform is a little complicated with ...
affy vsn limma written 14.6 years ago by Marcelo Luiz de Laia770 • updated 14.6 years ago by Sean Davis21k
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Answer: A: How extract F.p.value and lods values from a eBayes object in limma???
... Dear Mr Smyth, I am sorry, but I dont was clear in my subject question. I try to modify the subject now, to adjust it, but I was not capable to become it more clearly. Please, my excuses! I obtained to extract the individual values, but I would like to get them in an only table or archive togethe ...
written 14.7 years ago by Marcelo Luiz de Laia770

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Popular Question 13.2 years ago, created a question with more than 1,000 views. For Cannot find xml2-config

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