User: ncl.lazzarini

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Posts by ncl.lazzarini

<prev • 23 results • page 1 of 3 • next >
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Interpretation and analysis of lipids set
... I'm new to the analysis of lipidomics dataset. I extracted a set of "interesting" lipids (from a multivariate machine learning analysis). Now I'd like to evaluate those results from a biological point of view. When dealing with transcriptomics data the standard approach is to perform an **enrichment ...
lipidomics lipid enrichment validation written 23 months ago by ncl.lazzarini90
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Paired transcriptomics and lipidomics data
... I'm looking for some public available datasets that contains samples for which are available both transcriptomics and lipidomics data. In other words, I'd need, for the same sample both gene expression values and lipids abundance. Because I'll need to test some classification algorithms I also need ...
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Comment: C: Generic probe IDs to HUGO IDs API
... But you need to load the specific library: library("illuminaHumanv4.db") #Get this library if you don't have ...
written 2.7 years ago by ncl.lazzarini90
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Generic probe IDs to HUGO IDs API
... I'm working with microarray datasets. I usually convert the original probe ids to HUGO ids using online tools such as MadGene (http://cardioserve.nantes.inserm.fr/madtools/madgene/). Is there any API/tool that converts any type of probe IDs (e.g affymetrix: 114_r_at, Illumina: GI_10047089-S, ILMN_1 ...
probe hugo mapping api written 2.7 years ago by ncl.lazzarini90 • updated 2.6 years ago by Biostar ♦♦ 20
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Generator for synthetic microarray data
... Is there any tool (e.g R package or web-tool) that allows to generate synthetic microarray dataset? I've found MadSim(http://cran.r-project.org/web/packages/madsim/) for R that generates two biological conditions synthetic microarray dataset. Unfortunately is not possible to specify the number of sa ...
synthetic dataset artificial microarray omics written 3.7 years ago by ncl.lazzarini90
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Comment: C: Kaplan Meier curve to validate a set of biomarkers
... But what would be the meaning of each group? Let's suppose k=2 and there is a significant difference between the 2 KM curves? What can I conclude? What is the value of such division in groups? ...
written 3.9 years ago by ncl.lazzarini90
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Kaplan Meier curve to validate a set of biomarkers
... I have a set of biomarkers (genes) and I'd like to validate it analysing the Kaplan Meier survival curve. I had a look at the literature and most of the time this curve is calculated using the expression value of a single gene. The patients are divided in two groups:  low expression and high express ...
gene meier kaplan survival biomarkers written 3.9 years ago by ncl.lazzarini90 • updated 3.8 years ago by Biostar ♦♦ 20
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Best UPDATED tool for enrichment anlysis
... I have several gene sets and I'd like to perform an enrichment analysis in order to get GO terms, KEGG pathways and, possibly, PubMed IDs statistically overrepresented. I performed some analysis using DAVID. Unfortunately I noticed that DAVID is not up to date, in fact the last update of its knowled ...
gene enrichment set analysis tool written 4.0 years ago by ncl.lazzarini90 • updated 23 months ago by EagleEye5.8k
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Comment: C: David enrichment analysis inconsistency
... From the website it seems that the last update was on 2009 (5 years ago). I don't know exactly how the association between GO terms and gene works, but this means that some associations might have been deleted across the years right? ...
written 4.0 years ago by ncl.lazzarini90
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David enrichment analysis inconsistency
... I have a list of N genes. I used DAVID (http://david.abcc.ncifcrf.gov) in order to get the GO terms that are statistically overrepresented in that list. I selected the GO_BP_FAT subset of terms to not take in account some really generic GO terms (high level terms in the GO tree). Surprisingly I foun ...
gene enrichment analysis david ontology written 4.0 years ago by ncl.lazzarini90 • updated 3.4 years ago by Biostar ♦♦ 20

Latest awards to ncl.lazzarini

Popular Question 2.6 years ago, created a question with more than 1,000 views. For Expression values from Exon Array using affymetrix aroma
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Weighted Enrichment Analysis For Gene Networks
Popular Question 2.6 years ago, created a question with more than 1,000 views. For David enrichment analysis inconsistency
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Best UPDATED tool for enrichment anlysis
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Typical Microarray Data Probes Filtering
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Weighted Enrichment Analysis For Gene Networks
Popular Question 3.7 years ago, created a question with more than 1,000 views. For GO terms associated to a list of genes
Popular Question 3.7 years ago, created a question with more than 1,000 views. For GO terms depth level
Student 4.0 years ago, asked a question with at least 3 up-votes. For Expression values from Exon Array using affymetrix aroma

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