having problem to make Histogram graph with R for distribution of fpkm value per gene

Question

[hana]

I want to make the Histogram graph of distribution of fpkm value per gene from genes.fpkm_tracking (cufflinks out_put) file and then based on graph find the appropriate FPKM cutoff to identify the high express genes in my sample. I am not good in R , can you provide me the codes for this propose?

thanks in advance

[linus]

Why don't you first try it yourself and if you struggle you can come back either here or ask at stackoverflow?

This forum is not for ordering code.

Ps: this should not be a hard problem

[Sean Davis]

Hint: Use read.delim() and hist().

[Manvendra Singh]

Hint2: In the case if FPKM is in 10th coloumn of your read delim genes.fpkm_tracking

hist(genes.fpkm_tracking[,10], prob=TRUE)
lines(density(genes.fpkm_tracking[,10]))

just play around.

[hana]

Thank you so much for you help

Answer 1

[hana]

I have already made the density graph fpkm value per gene. Can any one let me know how I can choose of the appropriate fpkm cutoff based on the graph?

thank you

[Sean Davis]

You will need to determine that (and whether FPKM even makes sense to use) based on your experiment. There is no "right" cutoff.

[hana]

without graph, how can I choose the FPKM cutoff to identify the high express genes in my sample?