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Question: Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
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11 months ago by
hkarakurt10
hkarakurt10 wrote:

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. I used getGEO() command. When I used exprs() command, I have this message:

Error in (function (classes, fdef, mtable)  :
unable to find an inherited method for function ‘exprs’ for signature ‘"list"’

What is the real problem here? How can I find non-normalized expression matrix?

I also wanted to RAW data but there is not any RAW data file in supplementary section.

How can I reach RAW data, normalize it and find significantly changed genes. I really need help I am stuck.

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

Thank you.

modified 11 months ago by Sean Davis21k • written 11 months ago by hkarakurt10
1
11 months ago by
Aaron Lun20k
Cambridge, United Kingdom
Aaron Lun20k wrote:
2. Apply DE analysis workflows like https://bioconductor.org/help/workflows/RnaSeqGeneEdgeRQL/.
1
11 months ago by
Sean Davis21k
United States
Sean Davis21k wrote:

Echoing the answer by Aaron, here is the code to download all supplemental files for a given GEO accession.

library(GEOquery)
sfiles = getGEOSuppFiles('GSE80336')
fnames = rownames(sfiles)
# there is only one supplemental file


Yes there is only one supplement file and it is the Counts file. Mostly there are RAW_data files in supplemental files but this data is different. Probably I will use counts data for analyses.