meta-analysis of geo dataset

Question

[firstorthopedicdoctor]

I have downloaded multiple geodataset for one disease. How to combine genes in all dataset to calculate the differential gene expression in all datasets.

I HAVE TRIED CROSMETA BUT I had an error when exporting the geodataset as it mentions GSEID is not available. I even tried it on the data in the vignette and the error persists

I then tried metaintegrator but I faced this trouble and I have sent email to the authors and got no response

Here is the issue I have faced: https://github.com/cran/MetaIntegrator/issues/1

What other packages do you recommend?

[ATpoint]

Hi firstorthopedicdoctor,

generally you will see that users are reluctant to comment on questions that lack both details and do not contain any information on what you have already tried. Why not googling meta-analysis and either R-package or Bioconductor (the latter being the most prominent repository for bioinformatics R packages), then take the first hits and read the package documentations. Then come back with more specific questions. You need a background first.

Options could be:

https://bioconductor.org/packages/release/bioc/html/metaSeq.html

https://www.bioconductor.org/packages/release/bioc/html/metaArray.html

https://www.bioconductor.org/packages/release/bioc/html/metahdep.html

[firstorthopedicdoctor]

Done, I updated the question

[russhh]

Have you tried metap https://cran.r-project.org/web/packages/metap/index.html? It isn't designed specifically for expression datasets. [As an aside, the authors of MetaIntegrator probably aren't watching the github clone that you posted an issue to; so you might be better writing to the bioconductor support site]