## User: Riba Michela

Riba Michela80
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80
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Last seen:
2 years, 7 months ago
Joined:
5 years, 1 month ago
Email:
r***********@gmail.com

#### Posts by Riba Michela

<prev • 10 results • page 1 of 1 • next >
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... Hi, I found this stating from the page you mention Leading edge analysis and core enriched genes Leading edge analysis reports Tags to indicate the percentage of genes contributing to the enrichment score, List to indicate where in the list the enrichment score is attained and Signal for enrichmen ...
written 2.6 years ago by Riba Michela80
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... Oh sure, I have tried and as I told everything ok, consider the question is   how could I perform leading edge analysis using clusterprofiler? I tried the internal function just because I found the example gseDO in DOSE package, here: http://guangchuangyu.github.io/2016/05/news-of-my-bioc-packa ...
written 2.6 years ago by Riba Michela80
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... Hi,   I’m writing about your very useful and complete packages for functional analysis. In particular I often use DOSE and clusterProfiler and ChipSeeker.   I’m writing about the possibility to perform leading edge analysis in GSEA. I found on your github page you have already developed this  ...
written 2.6 years ago by Riba Michela80
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... Thanks a lot for explanations I'm pleased to go into more detail following the mail and studying! Thanks a lot so much Michela ...
written 5.0 years ago by Riba Michela80 • updated 4.1 years ago by Gordon Smyth37k
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... Hi, thanks for your quick answer, I get the point, and basically I actually arrived to the conclusion of being absorbed in the Intercept, for this reason I went on and put 0+ in the model, in any case sure I'm not a statistician, and I cannot move on from this. I'm not at the moment convinced abo ...
written 5.0 years ago by Riba Michela80 • updated 4.1 years ago by Gordon Smyth37k
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... Hi, I'm writing again dealing with a paired sample design: the experimental setting involves 9 patients, 3 disease stages and microarray expression data according to the included target file target<- readTargets("targetPT.txt") head(target) Genotype <- factor(target$Genotype) Disease<- fa ... written 5.0 years ago by Riba Michela80 • updated 4.1 years ago by Gordon Smyth37k 2 answers 1.3k views 2 answers ... Hi Professor Gordon, thanks for you answer. I just want to add some observations: -about the factor I actually declared as a factor, but afterwards I used another : >> r<-target$Condition #this should be numeric where actually I returned back to the target file and extracted the column o ...
written 5.1 years ago by Riba Michela80
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... Hi, thanks a lot for your answer and I'm forwarding the covariate matrix of our design. target<- readTargets("targetPTpGSp.txt") head(target) Genotype <- factor(target$Genotype) Disease<- factor(target$Disease, levels=c("stageA", "stageB", "stageC")) # Condition <-factor(target\$Con ...
written 5.1 years ago by Riba Michela80
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... Hi, thanks a lot for your kind answer. I have to specify an additional observation: the "r"parameter is indeed a numeric variable and also in this situation the result is the same. Would be reasonable to try and model the design as: design<- <- model.matrix(~0+r) #where "r"is a numeric variab ...
written 5.1 years ago by Riba Michela80
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... Hi, I'd like to start using CellMix package. I have my own data matrix from expression profiling using microarrays. Is it possible to use them instead of GEO datasets to make calculation? Is it sufficient to convert the matrix into an expressionSet object? And how could it be converted into an Expr ...
written 5.2 years ago by Riba Michela80

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