User: Ana Conesa

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Ana Conesa140
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Posts by Ana Conesa

<prev • 14 results • page 1 of 2 • next >
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Time series and RT-PCR
... Hi all, This is not a proper Bioconductor question, but I think this is a good forum to place my request. I am looking for a public/available dataset regarding to a Mutiple Series Time Course Microarray design, for which also Real Time -PCR data for a number of genes has been measured. Can anyone ...
microarray written 12.5 years ago by Ana Conesa140 • updated 12.5 years ago by Scott Ochsner300
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error with timecourse package
... I am trying to use the timecourse package to analyze gene expression data in a multiseries experiment with the following design: 3 time points (6,24,48 hrs) 5 biological conditions (1 to 5) 2665 genes 2 biological replicates per condition expect for the last one that has 6 re ...
timecourse written 12.7 years ago by Ana Conesa140
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Answer: A: Time course cDNA two color array analysis
... Hi Marcelo, I am not aware of GeneCycle and GeneNet, but maSigPro, limma, and I think timecourse also will take 2 color data. I do understand why you thought it was not possible. maSigPro will give you genes with changing expression profiles over time. You can follow the single series example given ...
written 12.8 years ago by Ana Conesa140
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Answer: A: question about maSigPro
... Yes, in principle you can replace Time by other quantitative variable. Ana On Tue, 5 Dec 2006 12:32:18 -0800 (PST), James Anderson wrote > Hi, > I am new to maSigPro, it seems to me that it is used mainly for > time series analysis, which allows another factor involved. My > question ...
written 13.0 years ago by Ana Conesa140
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Comment: C: microarray analysis of a dose response * strain experiment
... Hi Mark I recommend you to have a look to the maSigPro package and the corresponding publication (Bioinformatics 2006 22(9):1096-1102). The methodology has been designed for decting genes that change between experimental conditions on a data series, normally this would be different treatments along ...
written 13.0 years ago by Ana Conesa140
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Answer: A: OT: question about plots, general R, really...
... Hi Jose, I came across this same problem some time ago and I figured out a quite rudimentary solution, I guess. Probably there are more elgant ones (I would love to know them!!!) Basically what I do is: - Split my device up into one more row, very narrow, at the upper part, to host the general titl ...
written 13.4 years ago by Ana Conesa140
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Answer: A: Limma: combining 2 microarray studies
... Hi, I have been asked to analyze jointly two different microarray studies (2 color technology). They use the same microarray platform and represent the same biological process but each one follows a different experimental design and evaluate slightly different conditions One study has a reference d ...
written 13.6 years ago by Ana Conesa140
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Limma: combining 2 microarray studies
written 13.6 years ago by Ana Conesa140
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Answer: A: Limma and time-course data
... Dear Michael, You might want to have a look at the package maSigPro for the analysis of microarry time-course data. The method evaluates differences in gene expression along time and between experimetal conditions without focussing on specific time points, but analyzing gene expression trends. Ana ...
written 13.7 years ago by Ana Conesa140
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Limma: bad spots flagged out?
... Dear list, I have a doubt about the real use of spots weights during normalization in limma. According with the documentation spots weights equal to 0 are ignored during normalization (and other posterior analyses) , and although these spots are not removed they do ...
normalization limma written 13.7 years ago by Ana Conesa140

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