What kind of test in GEO2R ?

Question

[PNTick]

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/

[GenoMax]

More information here: https://www.ncbi.nlm.nih.gov/geo/info/geo2r.html#references

[PNTick]

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.

Answer 1

[ATpoint]

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

[PNTick]

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!

[ATpoint]

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.

[PNTick]

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.