This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Retrieving data from NCBI GEO and RNA-Seq Data Analysis

Hello, I am new at RNA-Seq data analysis and I want to analyze the data and do some analyses such as finding differentially expressed genes. My data set is from NCBI GEO and coded as GSE80336. Link is here:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80336

I see data is not normalized. How can I download the data from GEO with R, normalize it and make analyses? Is there a good pipeline for that?

Also there is a file called "Counts.txt" in supplementary. What is this file actually and can I use it?

Thank you.

rna-seq r geo normalization count
• 14,638 views • link
updated by Karma Karma • written by hkarakurt hkarakurt

1 answer

You can use the Bioconductor GEOquery package to retrieve / download datasets and platforms in R. You can normalize RNA-seq data a few different ways, so check out the Bioconductor Limma package. The counts file must be just that, the counts of each read. Of course you can use it, but should you use it for your analysis is a different question.

• 0 views • link
written by theobroma22 theobroma22

I tried to download it with getGEO() command but the expression matrix is empty. I used exprs() command for that. I am not sure how can I download non-normalized data.

• 0 views • link
written by hkarakurt hkarakurt

Can you post all of your code not just the functions you used. This will tell me which files you are trying to get from GSE80336, and why it is empty. Also, post any errors you may get too.

• 0 views • link
written by theobroma22 theobroma22

Log in to answer this question.

More posts like this