I have a project about RNA-seq. And I analyze the difference expression using cuffdiff.I have done the global statistics by R package CummeRbund.But I am puzzled about some of its funciton.
library("cummeRbund", lib.loc="D:/Program Files/R/R-3.0.0/library") setwd("F:/") cuff_data<- readCufflinks("AvsB") cuff_data CuffSet instance with: 2 samples 2708 genes 2723 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS csBoxplot(genes(cuff_data))
Now i got the figure as follows:
I reference the document "cummeRbund Visualization and Exploration of.pdf",But I find my figure is an exception.The legend of figure at reference is sample_name but condition for my figure.Beside ,I want to know the median, 1st quarter, 3rd quarter, the number of outlier of the boxplot, and I don't know how to get these .
This function has the same problem with the function csboxplot.Also it's starts from less than 0,but the figure in reference is starts from 0 and has a peak by the 0.
By the way my R version is 3.0.1.
EDIT: thanks for trying to improve the question.
This is one of the most poorly-written questions I have ever seen. Let me help you to improve it.
First, try to avoid "many questions." Try to identify a general theme which covers your problem. In your case, I'd suggest that you simply have not yet learned to use cummerbund properly. An informative title helps people understand your problem. "Something about cummerbund" is not a good title.
Second, link to examples. We don't know what a density image is, what you think it should look like, what yours looks like or how it differs to the image generated "by someone".
Third, avoid phrases like "and so on." What, precisely do you want to calculate and why, precisely, are you having difficulty? The last part of the question just sounds as though you want someone to tell you how to do more or less everything.
Now: please try to improve this question, or it will be closed/deleted.
I've modified my question.I will appreciate your comments.
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