statistics method to find the relation between multiple variables of 50 samples
Hi,
I have 50 samples and each sample has 3 variables (example data structure is as below)
Samples Var1 Var2 Var3
S1 10 5 2
S2 1 4 6
S2 5 4 0
. . . .
S50 2 1 10
What is the right statistics method to find the relation between theses variable and find out if there is a pattern in these variable?
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Other than pairwise correlation?
yes, I thought there might be some other new methods to work on it
Perhaps also look into PCA: https://en.m.wikipedia.org/wiki/Principal_component_analysis
I am mostly interested to see, say if variable 1 increases, what happens at variable 2, etc. I know that PCA can show the separation between the groups but I need some more detailed method
General simple test then - Spearman correlation, however, your distributions seems to be zero inflated and with many ties. Glm may help, but then you need to do plotting.
what exactly are these variables? maybe gene expression?
I actually am looking RNA-seq (FPKM (log2)), ATAC-seq data (Normalized RPKM ), and methylation % at 50 genes from one sample. Samples are my gene names and variables are RNA-seq, ATAC-seq, and methylation data. I wanna see the relation between these three data at these genes.
So you want to see if there is a linear model
gene ~ ATAC + methylation? Just put the data into a data.frame and uselm()Thank you very much! I just tried it
One question, I also tried cor(mydata). I am gonna read through this more in depth but do you think I should get the same result for cor and lm? (mine are different when I try these data)
See here about comparison of lm to cor: https://lindeloev.github.io/tests-as-linear/
The first method is plotting. Each variable separately and one against another. In r you should use functions plot(density(var)) and plot(var1, var2)
I will try it thanks
It may sound obvious, but it does worth time spent 100 percents - linear correlation is good only for some particular data distributions and only plotting may give you an intuition what is correct choice of the test (eg https://en.m.wikipedia.org/wiki/Anscombe%27s_quartet