Hello,

I have a data file that I want to run loess on for 36 columns, divide the original data by the new data, then dividing columns that end in A and B by those that end in C.  However, I have something wrong in my first step and am completely stuck on the third.  Could someone help me please?

Here's a snippet of the data file:
Order Target GC AA_001_A AA_001_B AA_001_C
1 a 0.584507042 422.94 302.32 412.19
2 b 0.630434783 193.44 182.88 224.96
3 c 0.649350649 132.67 116 136.12
4 d 0.635359116 306.78 203.68 306.98
5 e 0.609271523 276.32 214.73 307.03
6 f 0.626373626 333.93 249.28 421.97
7 g 0.618834081 216.22 200.94 236.27
All columns have 3722 rows.  The columns repeat in that pattern out to AA_012_C.

This is the script that I've tried:

gc<-read.delim("AA1_3_GC.txt")
gc2<-gc[,-c(1:2)]
res=cbind()
for(i in colnames(gc[,-1])){
                temp<-loess(i~GC,gc2)
                temp2<-predict(temp)
                if (length(res)==0){
                                res=temp2
                }else{ res=cbind(res,temp2)
                }
}

But I keep getting this error:
Error in model.frame.default(formula = i ~ GC, data = gc2) :
  variable lengths differ (found for 'GC')

If I manually type in a name, then it works just fine, but obviously I don't want to do that for 36 columns.  (Or 72 for the next project.)   Where am I going wrong and how to do I fix this?

For the second step (dividing column after I divide gc2/res), I really am unsure of where to even start.  I would guess that it would be something along the lines of
for(i in colnames(gc[,-1])){
        res[i]/res[i+2]}
But that would only get me A/C, then B/D, etc.  I've spent the last hour searching for this, but I'm clearly not using the right terms.  Could someone even point me in the right direction please?

Any help/suggestions you can give for either/both parts would be really appreciated.

Thanks,
Rose

 
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