More posts like this
-
Diference between Co-expressed gene-set enrichment analysis (COGENA) and gene-set enrichment analys…
written by omargmc.tak •Hello everybody, I have a doubt about which of these methods is better to have a gen ontology and pathway analysis. What I understand is …
-
Picking up differences in mutation sets
written by James •Hey all, As a non-biology guy working on a bioinformatics project, I wanted to ask the following. Suppose I have two groups of human tumor …
-
Python tools for gene annotation, ontology & gene set analysis
written by PianoEntropy •I'm a relative beginner in bioinformatics but have quite some experience with downstream analysis of scRNAseq data. Now I'm trying to do some gene ontology …
-
Genome alignment
written by Matt •Hey everyone, So, I'm having a little bit of trouble with some subjects. The first is understanding the importance of aligning the RNA-seq data to …
-
Doing multiple testing correction before or after GO analysis
written by c0tton •Hello, In a given RNA-Seq differential gene expression analysis, one might perform a gene ontology analysis by setting cutoffs to create a gene set (e.g. …
-
Methods to interrogate RNA-seq
written by telroyjatterLet's say you have an RNA-seq counts matrix for two experimental groups, and you have already generated your table of differentially expressed genes. Generally speaking, …
-
Determining Significance of Enrichment Analysis Within Clustering to Compare Clustering Methods
written by adavi140 •Hello, I have a dataset containing drugs and their corresponding indications. With such dataset, I used three different clustering methods to attempt to create groupings …
-
Stastical test for difference between TPMs for two transcript isoforms of a gene
written by jparker4 •Hi, I'm having some trouble knowing how best to test for statistical differences within my data. For each sample I mapped using salmon, I have …
-
No Go Terms For Genes When Using The Gostat Package In Bioconductor
written by shaikhfarahdeeba •<p>Hi can anybody plz help me regarding differential gene expression analysis i m using a dataset of affymetrix hgu133plus2 and carried out analysis using limma …
-
Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
written by sthait •<p>Hello,</p> <p>I'm working with biomaRt package in R. I'm trying to retreive all entrez genes of hsapiens<em>gene</em>ensembl data set. filtering by gene type - protein …
You forgot to post a question, or the problem you're having.
Hi
I have this code
GOenr=GOenrichmentAnalysis(moduleColors, allLLIDs, organism="mouse", nBestP=5);for the GOenrichmentAnalysisI'm having issues getting the results using Aracne, CLR to compare it with TOM, to see which network construction method is better. What do I need to do in order to get the results from different adjacency such as Aracne, CLR, etc.