Question: Clustering genes in time course analysis according slopes in quadratic regression model
gravatar for antgomo
5.1 years ago by
antgomo30 wrote:

I have a RNA time course experiment, 7 time points, 2 replicates per point. After analyzed with DESeq2 package, I want to subset my results in 4 categories

1. Those genes that are increasing expression lineally from time 0 to 7

2. Those genes that are decreasing expression lineally from time 0 to 7

3. Those genes that increase expression from 0 to 3/4 and then decrease

4. Those genes that decrease expression from 0 to 3/4 and then increase


So I fitted a quadratic regression model

      results<-apply(expression.matrix,1,function(x) lm(y~as.numeric(x)+I(as.numeric(x)^2)))

where y is a vector comprising time from 1 to 7 

Now I extract x and x2 from the results

   expression.matrix$x2<-unlist(lapply(results, function(x) return(x$coef[3])))
    expression.matrix$x<-unlist(lapply(results, function(x) return(x$coef[2])))

For class 1 ad 2 above, I know that with x >0 and x<0, I can get both, but for 3 and 4 , I don't know i have to take ( in case 3), x=0 and x2>0 and x=0 and x2<0 for 4. The problem is, that I don't have values of x of o, and even if got those ones closer to 0, the curve is not behaving as I expected


Any ideas?


Thanks in advance

ADD COMMENTlink modified 5.0 years ago by Biostar ♦♦ 20 • written 5.1 years ago by antgomo30

I would suggest fuzzy clustering with the mfuzz package in R.

ADD REPLYlink written 5.1 years ago by Benn8.1k
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