Relate to finding soft power, I ran "pickSoftThreshold" function and the result of that(sft) is as follow:
"Power" "SFT.R.sq" "slope" "truncated.R.sq" "mean.k." "median.k." "max.k."
"1" 1 0.30 0.92 0.89 2056.1 1903.5 4558.9
"2" 2 0.50 -1.52 0.91 548.1 445.5 1973.9
"3" 3 0.78 -2.05 0.96 188.3 128.3 1015.9
"4" 4 0.81 -2.21 0.97 77.21 42.3 594.9
"5" 5 0.82 -2.21 0.98 36.1 16.2 373.2
"6" 6 0.80 -2.18 0.96 18.8 6.9 245.8
"7" 7 0.78 -2.07 0.94 10.6 3.1 167.8
"8" 8 0.93 -1.75 0.99 6.4 1.5 121.7
"9" 9 0.94 -1.74 0.99 4.2 0.79 103.0
"10" 10 0.95 -1.69 0.99 2.87 0.42 88.2
"11" 12 0.97 -1.60 0.98 1.52 0.13 66.4
"12" 13 0.96 -1.56 0.98 1.17 0.07 58.7
"13" 14 0.96 -1.52 0.98 0.92 0.04 52.3
"14" 15 0.96 -1.48 0.98 0.75 0.02 46.9
"15" 16 0.95 -1.45 0.98 0.62 0.01 42.2
"16" 17 0.95 -1.41 0.98 0.53 0.01 38.1
"17" 18 0.95 -1.36 0.99 0.45 0.01 34.6
"18" 19 0.94 -1.33 0.99 0.40 0.00 31.5
My network type is 'Signed Hybrid' and cor type is 'bicor' as follows:
sft = pickSoftThreshold(datExpr, powerVector = powers, networkType = "signed hybrid", corFnc="bicor" ,corOptions = list(maxPOutliers =0.1), verbose = 5)
based on the sft result that I presented in this post and also mean connectivity plot, I selected power = 7 to construct a co-expression network for 5000 most connected genes and 58 colerectal cancer patients. Now, I have 5 modules as below:
green brown grey turquoise yellow
550 345 3400 610 95
As you see, 3400 genes are in the "grey" module. My question is that are these genes just in the "grey" module is reasonable? if it's not reasonable, how can I modify my constructing process? do the selected power as 7 is correct?
I really appreciated it if anybody share his/her comment with me.
