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Old 07-20-2013, 03:06 AM   #1
sazz
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Default Plotting replicate FPKMs in log10

Hello everyone,

I have 2 phenotypes (knockdown vs. control) and 3 replicates for each of them. All mapped and cuffdiff-ed. I want to get a plot between my replicates from same phenotypes with FPKM values on the x and y axis (in log10). Actually here is an example:



Can you suggest me a program for this purpose? I know you are going to say "R" but I am not very familiar with it.

Thanks!
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Old 07-20-2013, 04:05 AM   #2
DonDolowy
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Graphpad Prism. You can download a 30-days trial from their website. Excel can also do it.
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Old 07-20-2013, 09:05 AM   #3
dpryan
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Just because you're not currently familiar with R doesn't mean you can't become so! You'll probably have to familiarize yourself with R eventually anyway, if you're doing anything bioinformatics related.

Aside from that, any graphing program can make that graph.
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Old 07-20-2013, 09:44 AM   #4
sazz
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Thanks DonDolowy, Graphpad worked well for me, and dpryan, I totally agree with you about R issue, I need to learn it if I will be using those kind of programs.
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