java-GSEA rank gene list problem

If you have 2 groups(phenotypes) of sample, will GSEA calculate 2 different gene rank list? I mean if their rank list is the same(or reverse) their GSEA result should be the same, but the fact is not, java-GSEA will give results for each group(phenotype).

gsea

• 978 views • link

written 6.8 years ago by MatthewP

0 answers

No answers yet.

More posts like this

How to calculate inbreeding coefficient out of ROH (Plink)
written 1.9 years ago by t-ishige •

I calculate ROH with Plink. I have a question. My sample is two male groups and two female groups. How will the analysis be performed …
Differences between GSVA and GSEA?
written 3.4 years ago by DS •

What are the differences between GSVA and GSEA? I got some idea from a toward data science post ([link][1]): "GSVA builds on top of GSEA …
DESeq2 use of factors for colData
written 4.2 years ago by mcsimenc •

Hi, I am doing differential expression analysis using a count matrix with four samples and two groups using the function: `DESeqDataSetFromMatrix(countMatrix, colData = colData, design …
How do you interpret Tukey's significance when there is no group clustering alone?
written 4.9 years ago by DNAngel

I am confused by my results. I tested significance of means for 5 groups of my data and ANOVA confirmed there was a significant result …
GSEA for paired RNA-Seq data
written 6.9 years ago by bjeremy •

Hi all, I have samples from several individuals from two different time points (e.g., individual 1 day 1, individual 1 day 30, individual 2 day …
GSEA related to other functional analyses
written 9.0 years ago by sup230 •

Hi, I need clear explanation on how GSEA is related to other functional analyses in general. I understand that it tests whether an a priori …
Alternatives to Gene Set Enrichment Analysis dedicated for single samples
written 9.5 years ago by orzech_mag

Dear colleagues, I would like to perform Gene Set Enrichment Analysis (or some alternative analysis) on the data that contain only two samples, which represent …
understanding Cuffdiff comparison (or a general understanding of pair-wise v muti-groups comparisio…
written 10.9 years ago by CrazyB

<p>I have a general understanding of RNA-seq differential expression and some tools that are used to calculate the differential expression but was wondering if more …
GSEA Preranked analysis on RNA-SEQ
written 11.4 years ago by Ron

Hi all, I have done GSEA pre-ranked on differentially expressed genes between tumors and normals. The genes have been ordered by log fold change since …
What Is The Gene'S Correlation With Phenotype In Detail Using The Gsea
written 12.7 years ago by Zhilong Jia

<p>how to calculate the gene's correlation with phenotype in GSEA ?</p> <p>For example: two kinds of samples: Ctrl and Exper, GSEA will give a ranking …