User: Pierre-François Roux

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Posts by Pierre-François Roux

<prev • 12 results • page 1 of 2 • next >
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biomaRt - getBM() taking longer to run than usual ?
... Dear BioC community, I recently updated my R installation as well as all my BioC packages, including biomaRt. While before updated, the code bellow (for microarray probe annotation, 40k probes) ran in less than one minutes, it now takes more than half an hour. library(biomaRt) probes <- row. ...
biomart written 3 months ago by Pierre-François Roux0
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chipenrich - Error in .simpleInheritanceGeneric(fdef)
... Dear all, I use chipenrich for quite a long time now, and it always worked perfectly fine.  But for any reason, while trying to run it now, I get the following error : > library(chipenrich.data) > library(chipenrich) > > # Run ChipEnrich using an example dataset, assigning peaks to t ...
chipenrich written 2.0 years ago by Pierre-François Roux0
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Comment: C: oposSOM : additional parameters to setup the connexion to biomaRt ?
... Thanks for you answer Thomas. Indeed, I already noticed it was a known bug with the current Ensemble release, but I managed so far to work around. Nevertheless, I don't know if it is possible to do so when using the package oposSOM. Regards, Pierre-François ...
written 2.5 years ago by Pierre-François Roux0
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oposSOM : additional parameters to setup the connexion to biomaRt ?
... Dear all I am trying to use oposSOM to analyze Affymetrix HTA 2.0 array data. I assume that opsSOM is using the default host parameter when calling biomaRt. And the problem here is that, for any reason, using the current host, there is no HTA 2.0 annotation available. > Ensembl <- useMart( ...
biomart opossom written 2.5 years ago by Pierre-François Roux0 • updated 2.5 years ago by Thomas Maurel740
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Comment: C: Limma : design and contrast for a timecourse experiment with 2 cell lines
... Thanks a lot Aaron. This is far more clearer. Using this new model matrix, if I want to highlight genes exhibiting any time effect, I should use : any.time <- topTable(Fit2_LIMMA_Cell, coef = c(7:15), n=Inf, sort.by="none"). Am I right ?   Thx ! ...
written 2.8 years ago by Pierre-François Roux0
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Answer: A: Limma : design and contrast for a timecourse experiment with 2 cell lines
... Thank you so much Aaron for your precious advices. Using your approach to highlight variable genes whose change in expression is concordant between cell types, even if probably too conservative, gave nice results. Do you think about an alternative approach to Limma to address this question in a mor ...
written 2.8 years ago by Pierre-François Roux0
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Limma : design and contrast for a timecourse experiment with 2 cell lines
... Dear BioC list, I am currently working on a microarray timecourse experiment described bellow : Six time points, Two cell types A and B, No control experiment. Basically, I am studying the effect through time of a treatment on gene expressions in different cell lines. The biological question ...
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Answer: A: Csaw : filter windows based on matched negative control
... Hi Aaron, Thanks a lot for your answer.  In actual fact, I have 12 libraries, 6 that are samples and 6 that are inputs (2 samples and 2 inputs per condition). It wasn't that clear to me that using filterWindows(chip, control)will compare the average of all ChIP to the average of all input sample. ...
written 2.9 years ago by Pierre-François Roux0
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Csaw : filter windows based on matched negative control
...   Dear BioC users, I am currently using csaw to analyse my ChIP-seq data. For a given histone modification, I have 3 conditions, each with two biological replicates, and a matched input control library. Before going through the differential binding analysis, I would like to require a 3-fold or gre ...
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Comment: C: DiffBind : How is computed the correlation reported when using dba()
... Runing dba.count gave result closer to what I was expecting. > dba.count(Expe_K4Me1) Even if the information is different from the overlapping rate of called peaks between each replicates, it is interesting to consider it. Thanks again !   Pef     ...
written 3.3 years ago by Pierre-François Roux0

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