Hi all,
I'm very new to R and also RNA-seq in general so I hope my question is not too daft and that you might be able to help me out.
I have an experiment set up where I have a group of 8 samples. 2 x infected at 4hrs, 2 x mock infected at 4hrs, 2 x infected at 7hrs and 2 x mock infected at 7hrs.
I've been trying to use Deseq to analyse the read counts and by following the instructions from the PDF (which btw is very well written and can even be followed by a novice like me!) and I get to the point where I can look for differentially expressed genes. However, the instuctions only go into comparisons between two conditions. This is fine for looking at the infected and uninfected states but I would also like to examine whether the time course of infection has any effect on gene transcription. Is there any way of running a 3-way analysis in Deseq?
Also, when I come to display the results of the most significantly differentially expressed genes the table generated only produces the top 6 genes. Is there a way of exporting the whole table created so that i can introduce a cut-off myself based on p-values?
Thanks in advance for any help!
Emma
I'm very new to R and also RNA-seq in general so I hope my question is not too daft and that you might be able to help me out.
I have an experiment set up where I have a group of 8 samples. 2 x infected at 4hrs, 2 x mock infected at 4hrs, 2 x infected at 7hrs and 2 x mock infected at 7hrs.
I've been trying to use Deseq to analyse the read counts and by following the instructions from the PDF (which btw is very well written and can even be followed by a novice like me!) and I get to the point where I can look for differentially expressed genes. However, the instuctions only go into comparisons between two conditions. This is fine for looking at the infected and uninfected states but I would also like to examine whether the time course of infection has any effect on gene transcription. Is there any way of running a 3-way analysis in Deseq?
Also, when I come to display the results of the most significantly differentially expressed genes the table generated only produces the top 6 genes. Is there a way of exporting the whole table created so that i can introduce a cut-off myself based on p-values?
Thanks in advance for any help!
Emma
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