Hi all,
I have calculated the FPKM, but I don't know how to plot it in R properly.
The data starts with:
Col_10
25.2265
328.52
491.146
383.881
472.844
415.881
462.598
555.662
297.339
347.466
331.622
343.446
272.43
228.604
324.076
229.194
253.7
rna-seq
what do you want to show? You want to plot the FPKM against what?
density?
If you are only interested in the density of the FPKM (or the distribution), then you only need to use
histin R. You may also consider to log transform the data to make the axis shorted e.g.log10(FPKM)Can you write code for this? I don't know R. Starting from the reading data
I'm afraid that we would not be doing you a service by writing code for you. You should focus your attention on
read.table()andhist()in R and let us know if you get stuck.How to convert the vector data to numeric?
Great job. Google can help you with this one.
If you want help from us more directly, I'd suggest creating a new question, post some example input, the code you are trying, and the error message. This makes it clear what is working and what is not and makes the question much easier to answer.
Don't use FPKM.
why? what can I use FPKM instead?