how to begin the the Deseq2 analysis
Hello, I am learning Deseq2 analysis and I am having a problem to initiate this.
I have downloaded the data from GEO database in txt format and the imported it to R. Now how do I begin with Deseq2? i have tried few scripts but it is not working. The table after importing from Excel in R is given below. Also the entire table is not available.
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daverakshita •
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daverakshita •
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Should post this as a "question" rather than "tutorial". You are not giving a tutorial, you are asking a question about tutorial.
Second, the DESeq2 vignette is pretty thorough for output from different alignment pipelines.
Finally, give more details about your effort and what errors you got. 1) Show the header of your data 2) Show your commands 3) Show the errors generated.
Changed it to
Question.daverakshita, as per piyushjo, you can start with the DESeq2 vignette. However, if you have downloaded microarray data, then it is NOT suitable for analysis via DESeq2. limma is likely more appropriate.
If you want further help, please be very specific about the data that you have downloaded.