User: mattia pelizzola

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Posts by mattia pelizzola

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PhD program in Computational Biology in Milan, Italy
... *Applications are solicited for a PhD program in Computational Biology in Milan, Italy:* * * *Epigenome evolution in tumor models* (*Amati group, IIT & IEO*) Cancer originates from a complex combination of alterations at the level of the genome as well as of the epigenome. We are using next-ge ...
chipseq written 6.3 years ago by mattia pelizzola200
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occurrence of rGADEM motifs
... Hi, I am using rGADEM and MotIV to find out enriched motifs in my ChIPseq peaks and determine the similarity with Jaspar TFBS. These tools look very useful! rGADEM provides a list of enriched motifs. The total number of motifs is provided by the nOccurrences function, but I can't find a way to get ...
rgadem motiv written 6.3 years ago by mattia pelizzola200 • updated 6.3 years ago by Charles Joly Beauparlant150
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rtracklayer issues with other packages?
... Hi Martin, I am back on this rtracklayer issue after a while. There is a bug specifically when the package graph is loaded too (before or after rtracklayer). The code (apart from library(graph)) is from the rtracklayer vignette: > library(graph) > library(rtracklayer) Loading required packag ...
go cancer bsgenome graph biostrings gostats rtracklayer written 7.0 years ago by mattia pelizzola200 • updated 7.0 years ago by Michael Lawrence9.8k
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rtracklayer issues with other packages?
... Hi, I am running some code from the rtracklayer vignette. If I start a new R session and I load the rtracklayer only, the code works fine. Unfortunately, I need many other packages at the same time. For some reason when loading all the other packages I get this error: > data(targets) > targe ...
go bsgenome rtracklayer written 7.3 years ago by mattia pelizzola200 • updated 7.3 years ago by Martin Morgan ♦♦ 20k
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Comment: C: snow library, question on clusterExport
... thanks Martin for the explanations and thanks Norman for pointing out that error in the example, unfortunately I am still stuck with the main problem: I have to use clusterExport to export an object to the cluster nodes. clusterExport only seems to export objects from the GlobalEnv, unfortunately. ...
written 7.6 years ago by mattia pelizzola200
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snow library, question on clusterExport
... Hi, I have a simple function: > library(snow) > fun2=function() { + cl=makeCluster(3) + Mat=matrix(2:10,3,3) + fun3=function(startInd, endInd=3, data=Mat) {Mat[startInd:endInd,]} + print(clusterApplyLB(cl, 1:3, fun3)) + stopCluster(cl) + } that is working fine: > fun2() [[1]] [,1] ...
written 7.6 years ago by mattia pelizzola200 • updated 7.6 years ago by Pavelka, Norman70
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autocorrelation analysis
... Hi, I am trying to get some autocorrelation analysis based on positions of DNA words. Given a certain DNA motif or word, you can have its positions on the genome. I am trying to figure out if there is any regularity (pattern) in that. What I did is to determine pair-wise distances and see how many ...
written 8.5 years ago by mattia pelizzola200 • updated 8.5 years ago by Zeljko Debeljak50
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Answer: A: Further analysis after using MEDME?
... Dear Prashantha, for example you can select probes with significant methylation level in at least one sample. If AMSmat is the matrix with your AMS values for the four samples, you can do that filtering based on the max value for each probe, like: maxs=apply(AMSmat, 1, max, na.rm=T) dataF=AMSmat[m ...
written 8.5 years ago by mattia pelizzola200
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Answer: A: assistance to understand MEDME
... Hi, in the paper you can find that the MeDIP-chip enrichment is not linearly related with the DNA methylation level. MEDME is able to model this non-linear relationship using a calibration dataset where the genomic DNA is fully methylated. Limma is not used in MEDME. The only point where limma is m ...
written 8.6 years ago by mattia pelizzola200
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Answer: A: MEDME for MeDIP on Affymetrix promoter arrays
... Hi Adrian, the MEDME set can be built following the instructions on the MEDME reference manual (available on the MEDME bioc web page http://www.bioconductor.org/packages/release/bioc/html/MEDME.html) or available typing class?MEDMEset on the R GUI once MEDME is installed. You need to use: newSet= n ...
written 8.6 years ago by mattia pelizzola200

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