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Question: Making a table of RNA seq results
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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

ADD COMMENTlink 15 months ago tw617 • 30 • updated 15 months ago zx8754 7.5k
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I solved this problem. I made a data frame and sorted it by qvalues using order.

ADD COMMENTlink 15 months ago tw617 • 30
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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.

ADD COMMENTlink 15 months ago h.mon 25k
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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?

ADD REPLYlink 15 months ago
tw617
• 30

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