User: Eva Benito Garagorri

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6 years, 7 months ago
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Posts by Eva Benito Garagorri

<prev • 6 results • page 1 of 1 • next >
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Chip-Seq tag density plot
... Dear list, Hi again. Thank you once more for your input about the coverage plot. It has taken a bit but I finally got to try the idea Hervé proposed for calculating the coverage around the TSS. I know it's probably not very efficient since it uses a pretty long 'for' loop, but it works and it seem ...
coverage cancer written 6.6 years ago by Eva Benito Garagorri60
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Comment: C: Chip-Seq tag density plot
... Hervé, Vince, Thanks for your answers, I will give it a go and see how far I get. Best regards, Eva On 30/03/2011, at 22:21, Hervé Pagès wrote: > Hi Eva, > > One solution that involves a little bit of programming from your part > is to make those bins "by hand" by using things l ...
written 6.6 years ago by Eva Benito Garagorri60
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Chip-Seq tag density plot
... Dear list, I am trying to generate a tag density plot from a ChIP-Seq experiment for regions around the TSS of known transcripts. I suppose this is not too complicated, but I am having difficulties approaching this issue. I think maybe the most straightforward way is to use the GRanges capabilities ...
written 6.6 years ago by Eva Benito Garagorri60 • updated 6.6 years ago by Hervé Pagès ♦♦ 13k
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Comment: C: limma and minimum fold change
... Hi, First of all, I want to thank everyone for their kind answers. Thanks! I tried the conventional t-test after non-specific filtering on my data using the command "rowttests" from the "genefilter" package and that gives significant genes (after BH-adjustment) with a smaller fold change close to 1 ...
written 7.0 years ago by Eva Benito Garagorri60
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limma and minimum fold change
... Dear list, I have been working with some microarray data where I make simple comparisons between a control and a treatment group. I used vsn to normalize and limma to find differentially expressed genes. I used "topTable" with number=Inf and p.value=0.05 to get all significant genes for a given con ...
microarray vsn limma written 7.0 years ago by Eva Benito Garagorri60 • updated 7.0 years ago by Sean Davis21k
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BioNet - interpretation of node score
... Dear List, I have recently started exploring the Package ‘BioNet’ for network analysis of microarray data. I have a fundamental question about the interpretation of the results. From my understanding, BioNet first takes a series of p-values, fits them to a model, and then uses this information to ...
microarray visualization network bionet written 7.2 years ago by Eva Benito Garagorri60

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