Why the PCA results of PCASamples() from methylkit is different from prcomp()?
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Entering edit mode
18 months ago
maria2019 ▴ 170

I have the 'meth' object for my samples and I wanted to see more PCAs. I realized that PCs from PCASamples are different from what I calculate:

Using PCASamples():

library(methylKit)
meth <-readRDS(file="~/files/meth.rds")
pca <- PCASamples(meth, obj.return=TRUE)
pca$x
         PC1         PC2         PC3          PC4         PC5        PC6
sample1    54.7917242   78.835727 -146.389741  -88.0073775 -129.179034  -48.83519
sample2   45.8439749   79.986099 -132.748956 -115.7681777 -182.780012  -18.20983
sample3  -35.5084338  359.737490 -139.675979  340.2946409  178.827413  -49.74668
sample4    -0.8435795  169.940509  -87.345883   84.1664145   56.099736  -58.92960
  

Using prcomp():

library(methylKit)
meth <-readRDS(file="~/files/meth.rds")
mat=percMethylation(meth)
pca <- prcomp(mat)  
pca
             PC1           PC2         PC3           PC4         PC5
Sample1  -0.2238237  0.0888081766 -0.27426209  2.240539e-01 -0.128535081
Sample2  -0.2242289  0.0725052576 -0.26868740  2.560139e-01 -0.140892847
Sample3  -0.2227445 -0.0067194119 -0.45275679 -3.366611e-01  0.203404391
Sample4  -0.2230264  0.0068922158 -0.34130776 -2.185143e-01  0.139594741
  
methylkit prcomp pca PCASamples multiplePCA • 618 views
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1
Entering edit mode
18 months ago
maria2019 ▴ 170

I just realized that transpose=FALSE in PCASamples gives the same results as prcomp.

pca <- PCASamples(meth, obj.return=TRUE,transpose=FALSE) 
pca
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