distribution of fpkm value for gene

Question

[hana]

Hi, Iam a very new in RNA-Seq data analysis. How can I make the graph of distribution of fpkm value for genes in one sample.

Thanks in advance for your help

[hana]

Thanks for your reply

[hana]

thank you for your help

Answer 1

[lkmklsmn]

Gene expression levels (fpkm) can vary extremely. There will be many low expressed genes and a few very highly expressed genes. I would recommend log-scaling the X-axis in order to visualize this extreme range. Also good function in R, very similar to hist() is density().

[hana]

Thank you for your reply, I want to make the density graph of distribution of fpkm value for genes from genes.fpkm_tracking (cufflinks output) file for just one sample and then based on graph find the appropriate FPKM cutoff to identify the high express gens in my sample. I am not good in R, can you provide me the codes for this purpose

Thanks in advance

Answer 2

[Sean Davis]

The R stats package is really good at this type of thing. hist() might be a good place to start.