I am following this protocol for differential gene expression
https://kimlaborg.files.wordpress.com/2017/10/nprot-2016-095.pdf
In order to identify transcripts and genes with a q value <0.05 the following command in used
subset(results_transcripts,results_transcripts$qval<0.05)>subset(results_genes,results_genes$qval<0.05)
The Ballgown output is supposed to be appear in the form of table (2 tables in total, 1 for for genes and 1 for transcripts) on the screen for each of these commands as mentioned in protocol (Step16), but for my data nothing appear.
I am new to this field . I'll be really grateful if someone can guide me about how to get tables from these commands.
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Hello hirahameed222!
We believe that this post does not fit the main topic of this site.
This is purely an R question with almost no relevance to bioinformatics. Hint: Are you sure your data has rows where
qval<0.05?For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!