Hi,
I have RNA-seq data for 16 mouse samples. I would like to cluster cufflinks results of these samples by PCA in R. The data looks like this:
Commands in R:
How should I plot them in order to see clustered samples. I know my pca data are in data_pca$x, but how should I cluster them? and plot one point for each sample?
Thanks
I have RNA-seq data for 16 mouse samples. I would like to cluster cufflinks results of these samples by PCA in R. The data looks like this:
PHP Code:
gene_id gene_short_name FPKM_101 FPKM_102 FPKM_103 FPKM_104 FPKM_105 FPKM_106 FPKM_107 FPKM_108 FPKM_109 FPKM_110 FPKM_111 FPKM_112 FPKM_113 FPKM_114 FPKM_115 FPKM_116
uc007aeu.1 - 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
uc007aev.1 - 0 0 0.0095358 0.0095358 0.011704 1.48E-10 2.05E-63 0.0083273 0.014457 0.0068505 0.0053635 0.022235 0.0047757 0.018794 0 0.01661
uc007aew.1 - 0 0 0 0 0 1.2568 0.27389 0 0 0 0 0 0 0 0 0
uc007aex.2 - 0 0 0 0 0 7.1538 0.0096687 0 0 0 0 0 0 0 0.0050925 0
uc007aey.1 - 8.27E-07 0.00049201 0.00043141 0.00043141 0.00079353 0 0.00074324 1.56E-09 3.39E-20 1.16E-61 1.80E-20 1.72E-09 1.56E-96 5.13E-07 5.34E-07 4.78E-07
uc007afb.1 - 0.40549 2.08E-248 1.11E-19 1.11E-19 2.40E-93 0 0.49777 0.10711 1.22E-12 0.014644 6.48E-13 0.11777 0.02695 0.25169 0.08951 0.080144
uc007afc.1 - 1.93E-06 0.38845 0.34061 0.34061 0.31315 0 0 5.01E-09 1.04E-19 0.00046243 5.53E-20 5.51E-09 0.17202 1.20E-06 1.16E-06 1.04E-06
PHP Code:
data=read.csv('raw_cuff_data.csv', header=TRUE)
data_pca <- prcomp(data[, 3:18])
Thanks
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