Plotting replicate FPKMs in log10

sazz · 07-20-2013, 03:06 AM

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!

DonDolowy · 07-20-2013, 04:05 AM

Graphpad Prism. You can download a 30-days trial from their website. Excel can also do it.

dpryan · 07-20-2013, 09:05 AM

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.

sazz · 07-20-2013, 09:44 AM

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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07-20-2013, 03:06 AM	#1
sazz Member Location: Istanbul, Turkey Join Date: Oct 2012 Posts: 28	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!

07-20-2013, 04:05 AM	#2
DonDolowy Member Location: Freiburg Join Date: Oct 2012 Posts: 56	Graphpad Prism. You can download a 30-days trial from their website. Excel can also do it.

07-20-2013, 09:05 AM	#3
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	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.

07-20-2013, 09:44 AM	#4
sazz Member Location: Istanbul, Turkey Join Date: Oct 2012 Posts: 28	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.