Hi Everyone,
Disclaimer: I am very new to next gen sequencing / the Tuxedo suite of tools so please excuse gross incompetence!
I am using cummeRbund to visualize the results of my Cuffdiff run and while it is very impressive, I have a few questions about the figures it generates. I have 3 replicates of 5 conditions, each condition was compared head-to-head in 4 individual cuffdiff runs (this was done by our university's bioinformatics core).
I would like to take a selection of the most significant deferentially expressed genes and present it on a scatterplot. My workflow to accomplish this has been to look through gene_exp.diff in Excel, manually filter and sort as necessary, then pick my genes of interest and go back to R to create a gene set with these id's, then plot away. It works fine up to this point.
I can create the scatterplot, but it is of limited utility unlabeled. I would like to label each of the points (I'm only using about 20 genes in each set) with what gene it represents. Is this possible?
This would make my analysis much much easier than manually looking through the gene_exp.diff tables.
Please let me know if anyone has any suggestions or if I'm approaching this in the wrong way.
Thanks!
-orthodoc
Disclaimer: I am very new to next gen sequencing / the Tuxedo suite of tools so please excuse gross incompetence!
I am using cummeRbund to visualize the results of my Cuffdiff run and while it is very impressive, I have a few questions about the figures it generates. I have 3 replicates of 5 conditions, each condition was compared head-to-head in 4 individual cuffdiff runs (this was done by our university's bioinformatics core).
I would like to take a selection of the most significant deferentially expressed genes and present it on a scatterplot. My workflow to accomplish this has been to look through gene_exp.diff in Excel, manually filter and sort as necessary, then pick my genes of interest and go back to R to create a gene set with these id's, then plot away. It works fine up to this point.
I can create the scatterplot, but it is of limited utility unlabeled. I would like to label each of the points (I'm only using about 20 genes in each set) with what gene it represents. Is this possible?
This would make my analysis much much easier than manually looking through the gene_exp.diff tables.
Please let me know if anyone has any suggestions or if I'm approaching this in the wrong way.
Thanks!
-orthodoc
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