What kind of test in GEO2R ?
1
0
Entering edit mode
4 months ago
PNTick • 0

I am a beginner of bioinformatics. Today, I am trying to use GEO2R and get the Differential Expression Genes(DEGs) list. I could get the DEGs list sorted by "p-value".

My question is what kind of test is used in GEO2R. (student t-test? welch's t-test? DESeq? edgeR? Cuffdiff?)

I would appreciate it if someone could answer.

GEO2R : https://www.ncbi.nlm.nih.gov/geo/geo2r/

gene R • 248 views
ADD COMMENT
0
Entering edit mode
ADD REPLY
0
Entering edit mode

Thank you for answering my question. I checked and found the link "limma users guide". This page will provide me good information !

I appreciate your help.

ADD REPLY
1
Entering edit mode
4 months ago
ATpoint 49k

Neither, the tool runs the limma framework which is based on linear models and Empirical Bayes, see here the package at Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/limma.html

ADD COMMENT
0
Entering edit mode

Thank you for answering my question. I checked and found the PDF "usersguide.pdf". This page and the "limma users guide" page will provide me good information!

ADD REPLY
0
Entering edit mode

Sorry, but the concepts go beyond of what a single post here could cover. If you really want to dive into the math then I suggest you read the respective papers and get a background in linear algebra. For the end user though, properly reading the manual and applying the suggestions there will do just fine, you don't need to fully understand every concept to properly conduct an analysis, especially if outstanding documentation such as the one from limma exists.

ADD REPLY
0
Entering edit mode

Thank so much you for your reply. I will try to read the respective papers. And future, I would like to explain limma methods to others. I'll do my best!

Thank you for all your help.

ADD REPLY

Login before adding your answer.

Traffic: 2075 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6