Hello,
A simple question but I am just asking to make sure what I am doing is not wrong. I a want to analyze a published RNA-Seq dataset. The count file uploaded by the authors contains logCPM values from edger. I understand that DESEQ2 expects raw counts so I was wondering if I can use this count table with it? Would just raising all values to the power 10 and multiplying by a million generate the raw counts or is this the wrong approach?
Thanks
Thanks, their methods section just says the logCPM values were generated with edgeR but no other info is available.
Downloading and processing the raw data was something I was trying to avoid but it seems that might be the only way. I wonder why people dont upload raw counts though.
There are so many ways to generate raw counts and, as methods + annotation improve, quantification also improves. Raw counts does not mean raw data. Always start from raw data if you have the option to do so.
You can also do analysis of public RNA-seq datasets via tools like: https://maayanlab.cloud/biojupies/
Thanks. That is such a nice tool. Never knew something like this existed. I was able to find my dataset and generate the differential expression table in five minutes. I feel I will be using this a lot!