User: Maria Persico

gravatar for Maria Persico
Maria Persico100
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100
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Last seen:
13 years, 3 months ago
Joined:
14 years, 9 months ago
Email:
m****@cbm.bio.uniroma2.it

Posts by Maria Persico

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Run GOHyperG on yeast without specifying a chip
... thanks James, I though that the identifiers with wich you succeeded were the systematic names....for me common names were the other ones NOT belonging with Y. Best, Maria Maria Persico, PhD. student http://cbm.bio.uniroma2.it/~maria/ MINT database group Universita' di Tor Vergata, via della Ricer ...
written 13.3 years ago by Maria Persico100
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Run GOHyperG on yeast without specifying a chip
... Hello everyone, I'm trying to calculate the probability that 2 YEAST proteins share the same biological process by chance as suggested in the Liu's paper (PMID 15905281); I want a p-value associated to each protein pair in my data set; I would like to use the Bioconductor implementation of GO analy ...
microarray yeast process written 13.3 years ago by Maria Persico100 • updated 13.3 years ago by James W. MacDonald51k
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Comment: C: single-channel GenePix data
... Dear Bioconductor mailing list, I am explorying the two packages ScISI and y2hStat: the aim of these packages is to build an interactome starting from the available protein protein interaction datasets and combining them following a certain model. I would like to compare the interactome obtained wi ...
written 13.3 years ago by Maria Persico100
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Answer: A: Importing SMD data
... Hello, I'm using GraphAT package to "measure" the congruency between an experimental dataset and the metadata GO biological process. my experimental dataset is small if compared with GO meta data. The specie on which I'm working is Yeast(cerevisiae). The important absumption with the method "getp ...
written 14.1 years ago by Maria Persico100
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simLL method in GOstats to measure distances between yeast genes
... Dear All, I did some modifications in function simLL to allow this function access to ygs98 annotation: this is the code: simLL2<-function (ll1, ll2, Ontology = "MF", measure = "LP", dropCodes = NULL) { require(ygs98) #or library(ygs98) wh = match.arg(Ontology, c("MF", "BP", "CC")) ...
yeast hgu95av2 ygs98 written 14.4 years ago by Maria Persico100 • updated 14.4 years ago by rgentleman5.5k
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Comment: C: multtest problem...
... Dear Seth, dear Robert, thanks for your answers. I have still problems because I couldn't reinitialize goanal(sorry, I'm a beginner): indeed.... > goanal [1] "Error: invalid subscript type\n" attr(,"class") [1] "try-error" > str(goanal) Class 'try-error' chr "Error: invalid subscript type ...
written 14.5 years ago by Maria Persico100
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Comment: C: multtest problem...
... Dear bioconductor mailing list, I have some pairs of genes and I would like to measure their "distances" on the GO molecular function graph. So I wrote this lines of code: distances<-numeric(100) for (i in 1:100){ goanal<-simLL(as.character(hmapr$V1[i]),as.character(hmapr$V2[i]),"MF ") pr ...
written 14.5 years ago by Maria Persico100
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GOstats
... Hello to everybody, I have installed Version 2.0.1, and when I try to reproduce the example from the tutorial about GO in which the function GoHypherG is explained, I obtain this error message: xx<-GOHyperG(myLL, lib="hgu95av2", what="MF") Error in FUN(X[[50]], ...) : No direct or inherited m ...
go written 14.7 years ago by Maria Persico100 • updated 14.7 years ago by Sean Davis21k
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Comment: C: GOstats
... Thanks Sean, I did tmpLib <- tempfile() dir.create(tmpLib) install.packages2("GOstats",lib=tmpLib) and now it's ok. It's strange because when I installed R 2.0.1, I reinstall bioconductor. Maria Persico MINT database, Cesareni Group Universita' di Tor Vergata, via della Ricerca Scientifica ...
written 14.8 years ago by Maria Persico100
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GOstats
... Hello, I have installed Version 2.0.1, and when I try to load GOstats library I obtain this error message: > library(GOstats) Error in library(GOstats) : 'GOstats' is not a valid package -- installed < 2.0.0? where can I find makeGOGraph,oneGOGraph etc etc in this version of R? thank you fo ...
gostats written 14.8 years ago by Maria Persico100 • updated 14.8 years ago by Sean Davis21k

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