What is the difference between paired and unpaired and same.dir is true or false in Gage? · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

What is the difference between paired and unpaired and same.dir is true or false in Gage?

Hi Everyone

What is the difference between paired and unpaired and same.dir is true or false in Gage? I read the manual of gage but I still don't get it. If anyone can help me with a nice example. Gage will look for pathways any of my gene list are involved in, so what does it mean same direction or both, paired or not?

Thanks

rna-seq gage pathway analysis

• 1,592 views • link

written 8.7 years ago by Tania

0 answers

No answers yet.

Log in to answer this question.

More posts like this

What does it means, when 2-direction perturbed pathways are identified in the gage enrichment analy…
written 2.4 years ago by Assa Yeroslaviz

The `gage` method for enrichment analysis using ENTREZ Ids emphasizes on its capability to test for changes not only for up- and down-regulated pathways, but …
what is the insertPenalty for -U option of bwa mem?
written 3.9 years ago by yifangt86 •

Hello, I was trying to look at the scores of paired and unpaired alignments of my paired-end reads(FASTQ) on a reference with bwa mem. From …
Directionality of KEGG/Reactome/Wikipathways
written 8.0 years ago by chipolino •

Hi everyone, Am I right that pathways in KEGG do not have a direction? What I mean by that is for example pathway "KEGG_APOPTOSIS" contains …
which qvalue to use in pathway analysis using gage, same.dir?
written 8.3 years ago by Daisy •

**Hello Guys** If we use `same.dir = True` in Gage, we got the following stats: greater.p.geomean greater.stat.mean greater.p.val greater.q.val greater.set.size greater.exp1 less.p.geomean less.stat.mean less.p.val less.q.val …
problem plotting heatmap for pathways?
written 8.3 years ago by Sharon

Hi Everyone Does anyone know how can I fix the genedata function arguments to plot heatmap for my pathways? is not the rownames of keggres …
How can we find the list of genes involved in each pathway using Gage?
written 8.5 years ago by Tania

Hi all If we detected the pathways using gage, how can I find the list of genes involved in each pathway? I mean how to …
NA in pathways gage values
written 8.6 years ago by Tania

**Hi All** While printing my pathways, if I print my gobpres, many pathways are Nulls, do you know what is the reason of this? gobpres …
Up and down pathways are the same?
written 8.6 years ago by Tania

**Hello everyone** I am using gage to get the pathways of some affymatrix sets. The set of up and down pathways are the same but …
gage and pathview : genes are not mapped
written 8.7 years ago by Sharon

Hi Everyone I am new to using gage and pathway view to get some view about my genes. My edgeR genes are using symbols like …
cummeRbund grouping by TSS / CDS / Isoforms
written 8.8 years ago by corend

I am working on RNA-seq data with `cufflinks`. I now use `cummeRbund` to analyze my results. `cummeRbund` performs expression quantification between genes / isoforms / …