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Old 03-28-2012, 10:49 PM   #1
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Default Comparing densities of Chip-seq tag counts and plotting them

I have a matrix of Chip-seq results data like this for 26000 genes

LncRNA_ID LncRNA_Name Control_Raw_TagCount ICLIP_EZH2_Raw_TagCount
1 AK092525 47908 194887
2 ENST00000423879 RP11-12M5.1 10794 90146
3 AF318349 5514 61617
4 ENST00000506392 CTC-313D10.1 288 40880
5 ENST00000438080 RP11-177A2.4 25005 37380
6 AK123756 800 35469

I want to plot the counts densities of both samples, control and EZH2 in order to compare them. I am using R and I am very confused, mainly because I can't plot them as histograms, I get one figure with only one bar and not all the bars that I am waiting for, the same if I am interested to do a boxplot
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bioconductor, chip-seq, counts, density, tags

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