Importing data from GEO to R for analysing

[ruhi.vsg]

Dear all,

I hope you are doing well.

Firstly, I am sorry if my question looks naive, I am beginner in this field.

For importing data from GEO websit for RNA-seq, I use GEOquery library in R. Problem here is, some data are complete regarding RNA-seq data and meta data, but most of the data are defect without data which look weird for me.

For example: GSE149614, there is publication that authors used this data for their investigation. I used it for analyzing in R and importing it with GEOquery but there is no data after importing. I think maybe I am doing something wrong.

Can somebody help me with it?

bests,

[ruhi.vsg]

Something like this:

[seqadmin]

Hello ruhi.vsg. I'm not familiar with this, but I'm going to include your question in our newsletter so that others will see it and hopefully be able to help.

[SIA FLORENCE KOROMA]

Hello please i am new here, i need help on data

[SIA FLORENCE KOROMA]

i am working on PCR and qPCR real time data

[SIA FLORENCE KOROMA]

[email protected]

[fchatonnet]

Hello ruhi.vsg, GEOquery was originally released for micro-array data querying and analysis. Si using it to automatically retrieve bulk or single cell RNA-seq data might not be the best approach.
You might want to update R, BiocManager and GEOquery to their last versions, as a development version seems able to deal with RNA-seq data (but it might be bulk RNA-seq and not scRNA-seq...), see here: https://bioc.r-universe.dev/GEOquery/doc/manual.html
The install link provided is on github, not on Bioconductor, since its a devel version.
In the case of scRNA-seq data, you have to download the matrix and metadata files from GEO (provided they are available) by yourself and create your own R object by using a scRNA-seq analysis package such as Seurat, see answer from "haci" in https://bioinformatics.stackexchange...m-geo-database

Good luck!