Hello all,
After several days of moving through the TopHat Cufflinks workflow with the example fruit fly data (http://www.ncbi.nlm.nih.gov/pubmed/22383036), I have finally made it to CummeRbund.
When I execute the following commands in R, I get plots that are not the same as the ones found in the publication. Is that a problem?
library(cummeRbund)
cuff_data <- readCufflinks('diff_out')
csDensity(genes(cuff_data))
csScatter(genes(cuff_data), 'C1', 'C2')
csVolcano(genes(cuff_data), 'C1', 'C2')
Attached is the volcano plot. I just took a screen shot and saved it as ppt since I didn't know how to export or save the R graph.
Thanks and God bless,
Jason
After several days of moving through the TopHat Cufflinks workflow with the example fruit fly data (http://www.ncbi.nlm.nih.gov/pubmed/22383036), I have finally made it to CummeRbund.
When I execute the following commands in R, I get plots that are not the same as the ones found in the publication. Is that a problem?
library(cummeRbund)
cuff_data <- readCufflinks('diff_out')
csDensity(genes(cuff_data))
csScatter(genes(cuff_data), 'C1', 'C2')
csVolcano(genes(cuff_data), 'C1', 'C2')
Attached is the volcano plot. I just took a screen shot and saved it as ppt since I didn't know how to export or save the R graph.
Thanks and God bless,
Jason
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