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:
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?
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.