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

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

rna-seq
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updated by Ram Ram • written by hana hana

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

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updated by Ram Ram • written by linus linus

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

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updated by Ram Ram • written by Sean Davis Sean Davis

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.

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updated by Ram Ram • written by Manvendra Singh Manvendra Singh

Thank you so much for you help

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updated by Ram Ram • written by hana hana

1 answer

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

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updated by Ram Ram • written by hana hana

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

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updated by Ram Ram • written by Sean Davis Sean Davis

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

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written by hana hana

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