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1Rnwb

2010-Sep-27 19:47 UTC

[R] subtraction based on two groups in a dataframe

Hello 

I have a data set like below:
    plate.id well.id   Group      HYB  rlt1
1         P1      A1 Control SKOV3hyb 0.190
2         P1      A2 Control SKOV3hyb 0.210
3         P1      A3 Control SKOV3hyb 0.205
4         P1      A4 Control SKOV3hyb 0.206
5         P1      A5 Control SKOV3hyb 0.184
385       P1      A1    ovca SKOV3hyb 0.184
386       P1      A2    ovca SKOV3hyb 0.229
387       P1      A3    ovca SKOV3hyb 0.214
388       P1      A4    ovca SKOV3hyb 0.226
389       P1      A5    ovca SKOV3hyb 0.217
390       P1      A6    ovca SKOV3hyb 0.207


each plate.id contains 384 readings for Group=="Control" and the same
plate.id will contain 384 readings for Group=='ovca' to give a total of
768
values for P1 and so on for other plate ID's. I have to take the subtract
the values of rlt1 colum between the two groups based on Plate ID.

currently I am using> newdat2$diff<-(newdat2[1:5,5]-newdat2[6:10,5])/newdat2[1:5,5]*100
> newdat2    plate.id well.id   Group      HYB  rlt1       diff
1         P1      A1 Control SKOV3hyb 0.190   3.157895
2         P1      A2 Control SKOV3hyb 0.210  -9.047619
3         P1      A3 Control SKOV3hyb 0.205  -4.390244
4         P1      A4 Control SKOV3hyb 0.206  -9.708738
5         P1      A5 Control SKOV3hyb 0.184 -17.934783
385       P1      A1    ovca SKOV3hyb 0.184   3.157895
386       P1      A2    ovca SKOV3hyb 0.229  -9.047619
387       P1      A3    ovca SKOV3hyb 0.214  -4.390244
388       P1      A4    ovca SKOV3hyb 0.226  -9.708738
389       P1      A5    ovca SKOV3hyb 0.217 -17.934783

I have tried 
apply(newdat2, 1, function(x) tapply(x, plate.id,
newdat2$Control-newdat2$ovca)))

I am looking for a more simple way to calculate the percent difference
between the each value (based on well.id) for the two groups for 100's of
plate.ids.

I would appreciate help in getting this solved.
Thanks

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Remko Duursma

2010-Sep-28 01:12 UTC

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[R] subtraction based on two groups in a dataframe

Try something like this:



dfr <- read.table(textConnection("    plate.id well.id   Group      HYB 
rlt1 
1         P1      A1 Control SKOV3hyb 0.190 
2         P1      A2 Control SKOV3hyb 0.210 
3         P1      A3 Control SKOV3hyb 0.205 
4         P1      A4 Control SKOV3hyb 0.206 
5         P1      A5 Control SKOV3hyb 0.184 
385       P1      A1    ovca SKOV3hyb 0.184 
386       P1      A2    ovca SKOV3hyb 0.229 
387       P1      A3    ovca SKOV3hyb 0.214 
388       P1      A4    ovca SKOV3hyb 0.226 
389       P1      A5    ovca SKOV3hyb 0.217 "))


difs <- lapply(split(dfr,dfr$plate.id), function(x)x$rlt1[x$Group
="Control"] - x$rlt1[x$Group == "ovca"])
dfr$Diff <- Reduce(c,difs)



greetings,
Remko
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Dennis Murphy

2010-Sep-28 10:58 UTC

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[R] subtraction based on two groups in a dataframe

Hi:

Perhaps this might be useful:

tst <- read.table(textConnection("
+    plate.id well.id  Group      HYB  rlt1
+ 1         P1      A1 Control SKOV3hyb 0.190
+ 2         P1      A2 Control SKOV3hyb 0.210
+ 3         P1      A3 Control SKOV3hyb 0.205
+ 4         P1      A4 Control SKOV3hyb 0.206
+ 5         P1      A5 Control SKOV3hyb 0.184
+ 385       P1      A1    ovca SKOV3hyb 0.184
+ 386       P1      A2    ovca SKOV3hyb 0.229
+ 387       P1      A3    ovca SKOV3hyb 0.214
+ 388       P1      A4    ovca SKOV3hyb 0.226
+ 389       P1      A5    ovca SKOV3hyb 0.217"), header = TRUE)

tst2 <- reshape(tst, idvar = c('plate.id', 'well.id'),
timevar = 'Group',
                 direction = 'wide')
tst2
  plate.id well.id HYB.Control rlt1.Control HYB.ovca rlt1.ovca
1       P1      A1    SKOV3hyb        0.190 SKOV3hyb     0.184
2       P1      A2    SKOV3hyb        0.210 SKOV3hyb     0.229
3       P1      A3    SKOV3hyb        0.205 SKOV3hyb     0.214
4       P1      A4    SKOV3hyb        0.206 SKOV3hyb     0.226
5       P1      A5    SKOV3hyb        0.184 SKOV3hyb     0.217

tst2$rlt1.diff <- rlt1.ovca - rlt1.Control

reshape() is reshaping the data based on plate.id * well.id combinations, so
the observations in Control and ovca should match on those two keys..

HTH,
Dennis


On Mon, Sep 27, 2010 at 12:47 PM, 1Rnwb <sbpurohit@gmail.com> wrote:
>
> Hello
>
> I have a data set like below:
>    plate.id well.id   Group      HYB  rlt1
> 1         P1      A1 Control SKOV3hyb 0.190
> 2         P1      A2 Control SKOV3hyb 0.210
> 3         P1      A3 Control SKOV3hyb 0.205
> 4         P1      A4 Control SKOV3hyb 0.206
> 5         P1      A5 Control SKOV3hyb 0.184
> 385       P1      A1    ovca SKOV3hyb 0.184
> 386       P1      A2    ovca SKOV3hyb 0.229
> 387       P1      A3    ovca SKOV3hyb 0.214
> 388       P1      A4    ovca SKOV3hyb 0.226
> 389       P1      A5    ovca SKOV3hyb 0.217
> 390       P1      A6    ovca SKOV3hyb 0.207
>
>
> each plate.id contains 384 readings for Group=="Control" and the
same
> plate.id will contain 384 readings for Group=='ovca' to give a
total of
> 768
> values for P1 and so on for other plate ID's. I have to take the
subtract
> the values of rlt1 colum between the two groups based on Plate ID.
>
> currently I am using
> > newdat2$diff<-(newdat2[1:5,5]-newdat2[6:10,5])/newdat2[1:5,5]*100
> > newdat2
>    plate.id well.id   Group      HYB  rlt1       diff
> 1         P1      A1 Control SKOV3hyb 0.190   3.157895
> 2         P1      A2 Control SKOV3hyb 0.210  -9.047619
> 3         P1      A3 Control SKOV3hyb 0.205  -4.390244
> 4         P1      A4 Control SKOV3hyb 0.206  -9.708738
> 5         P1      A5 Control SKOV3hyb 0.184 -17.934783
> 385       P1      A1    ovca SKOV3hyb 0.184   3.157895
> 386       P1      A2    ovca SKOV3hyb 0.229  -9.047619
> 387       P1      A3    ovca SKOV3hyb 0.214  -4.390244
> 388       P1      A4    ovca SKOV3hyb 0.226  -9.708738
> 389       P1      A5    ovca SKOV3hyb 0.217 -17.934783
>
> I have tried
> apply(newdat2, 1, function(x) tapply(x, plate.id,
> newdat2$Control-newdat2$ovca)))
>
> I am looking for a more simple way to calculate the percent difference
> between the each value (based on well.id) for the two groups for 100's
of
> plate.ids.
>
> I would appreciate help in getting this solved.
> Thanks
>
> --
> View this message in context:
>
http://r.789695.n4.nabble.com/subtraction-based-on-two-groups-in-a-dataframe-tp2716104p2716104.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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