Question: how to interpret NES(normalized enrichment score)?
0
gravatar for ghmdsr
2.4 years ago by
ghmdsr40
ghmdsr40 wrote:

hi i'm first-year graduate student.

I got the result of my analysis in which NES is included.

I wonder about the meaning of positive score/negative score of NES.

I know that NES negative score means weaker relative activity in a sample compared with the background population, and positive score means greater relative activity .

I ask you that

  1. if i got negative NES, that means nonrespondent have weaker relative activity than respondent group.

  2. if i change first column(nonres) with second column(res),

    negative NES -> respondent group have weaker relative activity than nonrespondent group??

    In a nut shell, can i interpret the result depending on design matrix??


<designmatrix> 


here is my desigmatrix of my 5 samples.

nonres res
   0      1
   1      0
   1      0
   1      0
   0      1
rna-seq R gene • 6.5k views
ADD COMMENTlink modified 20 months ago by johnsonnathant80 • written 2.4 years ago by ghmdsr40
0
gravatar for Pietro
20 months ago by
Pietro100
Italy
Pietro100 wrote:

Maybe it's not super clear, but try to have a look at this question about GSEA

ADD COMMENTlink written 20 months ago by Pietro100
0
gravatar for johnsonnathant
20 months ago by
United States
johnsonnathant80 wrote:

I assume the 'NES' type abbreviation is coming from the GSEA analysis that can be commonly run via R (https://bioconductor.org/packages/release/bioc/html/fgsea.html) that was made popular through the BROAD (http://software.broadinstitute.org/gsea/index.jsp). Since its not completely obvious what it stands for here is the definition:

NES = enrichment score normalized to mean enrichment of random samples of the same size

Meaning, the enrichment score given normalized based on the number of genes in the gene set, 'same size' is the key descriptor in the explanation. Hope that helps!

ADD COMMENTlink written 20 months ago by johnsonnathant80

This is not correct - it's normalized to the mean enrichment of random samples of the same size. The method employs random sampling of gene sets of the same size as the gene set being tested to assess significance and for normalization. The number of samplings is specified as a parameter.

ADD REPLYlink written 18 months ago by sliders70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 799 users visited in the last hour