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I think this is not enough information for a qualified answer. What is your goal? What do you want to find? Are you looking for differences or similarities in the data? Are the samples dependent? etc etc etc
I have some RNA-seq data(control/treatment) of effecting some drug on different cancer, I did differential expression analysis (with CLC Genomics)(genes and lncRNA) of each experiments and now I want to do meta analysis with R,but I do not know what should I do. I hope my explanation is clear enough for you.
No, it is clearly not enough information... it is just a rephrasing of the initial limited piece of information. Please take a break and thing about your actual question. I doubt that anyone can help without you specifying an exact question.
Here are some examples for "meta-analysis" but I have absolutely no clue if this is what you are thinking about:
Please discuss the scientific question with your PI. If you know what you want to investigate, someone on Biostars might be able (and willing) to help you...
thank you for your attention and suggestion dear Manuel,I should do meta analysis for genes with low p-values and high fold change that I receive from different experiments (it is clear that there are not same from different experiment),this idea is not true?
it is clear that there are not same from different experiment
This is not true. For example, if your drug is inhibiting the activity of a protein and the protein is regulating the expression of some genes you would expect to find a down- or up-regulation of the target genes in all samples similarly. Therefore a "meta-analysis" to identify genes which receive a low p-Value throughout all experiments is a valid target question given the sparse information you provided. And it is the exact example, why we need more information on your scientific question if you want us to help.
Therefore, please provide detailed information, which scientific question you want to investigate with your "meta-analysis" and how your experimental setup was. As I tried to explain, there are thousands of different kinds of "meta-analyses" and thousands of different questions you can target with a "meta-analysis".
I do not have any idea that what I can do with meta analysis by these data ,only I know I should study effect of some drug on some cancer.
If you don't know the question, how can you expect us to know the answer?!
Read some papers in your field, to do some basic research on what is possible, ask your PI on examples of meta-analysis that she/he found interesting as template, and then try to figure out what you want to investigate. Simply doing some kind of whatsoever-analysis just because one can is not appropriate and a waste of time.
I am out of this discussion because it is a waste of my time. All the best and good luck