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Question: Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
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gravatar for hkarakurt
14 months ago by
hkarakurt20
hkarakurt20 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. 

Should I start with SRA files?

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

Thank you.

ADD COMMENTlink modified 14 months ago by Sean Davis21k • written 14 months ago by hkarakurt20
1
gravatar for Aaron Lun
14 months ago by
Aaron Lun21k
Cambridge, United Kingdom
Aaron Lun21k wrote:
  1. Download the "Counts.txt" supplementary file, which contains... counts, unsurprisingly enough.
  2. Apply DE analysis workflows like https://bioconductor.org/help/workflows/RnaSeqGeneEdgeRQL/.
ADD COMMENTlink written 14 months ago by Aaron Lun21k
1
gravatar for Sean Davis
14 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
b2 = read.delim(fnames[1],header=TRUE)
head(b2)
ADD COMMENTlink written 14 months ago by Sean Davis21k

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.

Thank you for answer.

ADD REPLYlink written 14 months ago by hkarakurt20
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