This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Making a table of RNA seq results

I used exacttest (edgeR) on some RNA seq data. I need to make a table that depicts the 10 genes with the smallest q- values, their log fold change, and their raw expression values. I have the q-values stored in a numeric vector, the fold change can be found by using exacttest$table$logFC, and I have the raw expression values .

I am not sure how to put all of these together in a table and sort them. I tried sorting the q-values using sort(qvalues), this certainly displays the top 10 smallest qvalues but in the vector they are not associated with a gene ID so I don't think I can do this. Any ideas on how to do this?

Thanks

r rna-seq edger
• 1,812 views • link
updated by zx8754 zx8754 • written by tw617 • tw617

2 answers

I solved this problem. I made a data frame and sorted it by qvalues using order.

• 1 views • link
written by tw617 • tw617

Why you have a vector of q-values? exacttest output already includes multiple testing correction - the exacttest$table$FDR column. You can find and extract the function topTags.

• 1 views • link
written by h.mon h.mon

Thank you for the reply, I solved my problem in the meantime. I had to do it this certain way as part of an assignment. I don't see $FDR as an option, perhaps I need to load another package to have that feature?

• 1 views • link
written by tw617 • tw617

Log in to answer this question.

More posts like this