Re: [R] subtraction based on two groups in a dataframe
I want the reshaped data to look like this.
plate.id HYBwell.id rlt1.control1
well.id rlt1.control1 well.idrlt1.disease1 well.id
rlt1.disease2
1 P1 SKOV3hyb A10.190
A2 0.210 B10.217B2
0.190
2P1 SKOV3hyb A3 0.205
A4 0.206 B30.371B4
0.56
Thanks
Sharad
On Thu, Oct 7, 2010 at 7:09 PM, djmuseR [via R] <
ml-node+2967676-1432920781-6...@n4.nabble.com
> wrote:
> Hi:
>
> Is this what you were looking for?
>
> plate.id well.id Group HYB rlt1
> P1 A1 control1SKOV3hyb0.19
> P1 A2 disease1SKOV3hyb0.21
> P1 A3 control1SKOV3hyb0.205
> P1 A4 disease1SKOV3hyb0.206
> P1 B1 disease2SKOV3hyb0.217
> P1 B2 control2SKOV3hyb0.646
> P1 B3 disease2SKOV3hyb0.371
> P1 B4 control2SKOV3hyb
>
> dfwide <- reshape(df, idvar = c('plate.id', 'well.id', 'HYB'), timevar =
> 'Group',
> direction = 'wide')
> > dfwide
> plate.id well.id HYB rlt1.control1 rlt1.disease1 rlt1.disease2
> 1 P1 A1 SKOV3hyb 0.190NANA
> 2 P1 A2 SKOV3hybNA 0.210NA
> 3 P1 A3 SKOV3hyb 0.205NANA
> 4 P1 A4 SKOV3hybNA 0.206NA
> 5 P1 B1 SKOV3hybNANA 0.217
> 6 P1 B2 SKOV3hybNANANA
> 7 P1 B3 SKOV3hybNANA 0.371
> 8 P1 B4 SKOV3hybNANANA
> rlt1.control2
> 1NA
> 2NA
> 3NA
> 4NA
> 5NA
> 6 0.646
> 7NA
> 8 0.560
>
>
> HTH,
> Dennis
>
> On Thu, Oct 7, 2010 at 7:54 AM, 1Rnwb <[hidden
> email]>
> wrote:
>
> >
> > Hi The reshape suggestions works great on my previous data, but I am
> unable
> > to make is work on the new dataset. It actually works but only gives me
> the
> > output of single row, instead of 96 rows.
> > The dataset has two control groups control 1 and control 2, two disease
> > groups viz disease 1 and disease 2 a total of 384 values
> > plate.idwell.id Group HYB rlt1
> > P1 A1 control1SKOV3hyb0.19
> > P1 A2 disease1SKOV3hyb0.21
> > P1 A3 control1SKOV3hyb0.205
> > P1 A4 disease1SKOV3hyb0.206
> > P1 B1 disease2SKOV3hyb0.217
> > P1 B2 control2SKOV3hyb0.646
> > P1 B3 disease2SKOV3hyb0.371
> > P1 B4 control2SKOV3hyb0.56
> >
> > when I use
> > ydat <- reshape(ydat, idvar = c('plate.id','HYB'), timevar
> > ='Group',direction = 'wide')
> >
> > I get
> >
> > plate.idwell.id.control1HYB.control1rlt1.control1
> > well.id.disease1
> > HYB.disease1rlt1.disease1 well.id.disease2HYB.disease2
> > rlt1.disease2
> > well.id.control2HYB.control2rlt1.control2
> > P1 A1 SKOV3hyb0.19A2 SKOV3hyb0.21
> B1
> > SKOV3hyb0.217 B2 SKOV3hyb0.646
> >
> >
> > instead of 96 rows of data, only one row comes, i tried new.row.names but
>
> > that is not working.
> > I would appreciate the help.
> > Thanks
> >
> > --
> > View this message in context:
> >
> http://r.789695.n4.nabble.com/subtraction-based-on-two-groups-in-a-dataframe-tp2716104p2966918.html
> > Sent from the R help mailing list archive at Nabble.com.
> >
> > __
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> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> [[alternative HTML version deleted]]
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Re: [R] subtraction based on two groups in a dataframe
Hi:
Is this what you were looking for?
plate.id well.id Group HYB rlt1
P1 A1 control1SKOV3hyb0.19
P1 A2 disease1SKOV3hyb0.21
P1 A3 control1SKOV3hyb0.205
P1 A4 disease1SKOV3hyb0.206
P1 B1 disease2SKOV3hyb0.217
P1 B2 control2SKOV3hyb0.646
P1 B3 disease2SKOV3hyb0.371
P1 B4 control2SKOV3hyb0.56
dfwide <- reshape(df, idvar = c('plate.id', 'well.id', 'HYB'), timevar =
'Group',
direction = 'wide')
> dfwide
plate.id well.id HYB rlt1.control1 rlt1.disease1 rlt1.disease2
1 P1 A1 SKOV3hyb 0.190NANA
2 P1 A2 SKOV3hybNA 0.210NA
3 P1 A3 SKOV3hyb 0.205NANA
4 P1 A4 SKOV3hybNA 0.206NA
5 P1 B1 SKOV3hybNANA 0.217
6 P1 B2 SKOV3hybNANANA
7 P1 B3 SKOV3hybNANA 0.371
8 P1 B4 SKOV3hybNANANA
rlt1.control2
1NA
2NA
3NA
4NA
5NA
6 0.646
7NA
8 0.560
HTH,
Dennis
On Thu, Oct 7, 2010 at 7:54 AM, 1Rnwb wrote:
>
> Hi The reshape suggestions works great on my previous data, but I am unable
> to make is work on the new dataset. It actually works but only gives me the
> output of single row, instead of 96 rows.
> The dataset has two control groups control 1 and control 2, two disease
> groups viz disease 1 and disease 2 a total of 384 values
> plate.idwell.id Group HYB rlt1
> P1 A1 control1SKOV3hyb0.19
> P1 A2 disease1SKOV3hyb0.21
> P1 A3 control1SKOV3hyb0.205
> P1 A4 disease1SKOV3hyb0.206
> P1 B1 disease2SKOV3hyb0.217
> P1 B2 control2SKOV3hyb0.646
> P1 B3 disease2SKOV3hyb0.371
> P1 B4 control2SKOV3hyb0.56
>
> when I use
> ydat <- reshape(ydat, idvar = c('plate.id','HYB'), timevar
> ='Group',direction = 'wide')
>
> I get
>
> plate.idwell.id.control1HYB.control1rlt1.control1
> well.id.disease1
> HYB.disease1rlt1.disease1 well.id.disease2HYB.disease2
> rlt1.disease2
> well.id.control2HYB.control2rlt1.control2
> P1 A1 SKOV3hyb0.19A2 SKOV3hyb0.21B1
> SKOV3hyb0.217 B2 SKOV3hyb0.646
>
>
> instead of 96 rows of data, only one row comes, i tried new.row.names but
> that is not working.
> I would appreciate the help.
> Thanks
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/subtraction-based-on-two-groups-in-a-dataframe-tp2716104p2966918.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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Re: [R] subtraction based on two groups in a dataframe
Hi The reshape suggestions works great on my previous data, but I am unable
to make is work on the new dataset. It actually works but only gives me the
output of single row, instead of 96 rows.
The dataset has two control groups control 1 and control 2, two disease
groups viz disease 1 and disease 2 a total of 384 values
plate.idwell.id Group HYB rlt1
P1 A1 control1SKOV3hyb0.19
P1 A2 disease1SKOV3hyb0.21
P1 A3 control1SKOV3hyb0.205
P1 A4 disease1SKOV3hyb0.206
P1 B1 disease2SKOV3hyb0.217
P1 B2 control2SKOV3hyb0.646
P1 B3 disease2SKOV3hyb0.371
P1 B4 control2SKOV3hyb0.56
when I use
ydat <- reshape(ydat, idvar = c('plate.id','HYB'), timevar
='Group',direction = 'wide')
I get
plate.idwell.id.control1HYB.control1rlt1.control1
well.id.disease1
HYB.disease1rlt1.disease1 well.id.disease2HYB.disease2
rlt1.disease2
well.id.control2HYB.control2rlt1.control2
P1 A1 SKOV3hyb0.19A2 SKOV3hyb0.21B1
SKOV3hyb0.217 B2 SKOV3hyb0.646
instead of 96 rows of data, only one row comes, i tried new.row.names but
that is not working.
I would appreciate the help.
Thanks
--
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http://r.789695.n4.nabble.com/subtraction-based-on-two-groups-in-a-dataframe-tp2716104p2966918.html
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Re: [R] subtraction based on two groups in a dataframe
Thanks for the help.
Sharad
On Mon, Sep 27, 2010 at 9:12 PM, Remko Duursma [via R] <
ml-node+2716469-935075351-6...@n4.nabble.com
> wrote:
> 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 A1ovca SKOV3hyb 0.184
> 386 P1 A2ovca SKOV3hyb 0.229
> 387 P1 A3ovca SKOV3hyb 0.214
> 388 P1 A4ovca SKOV3hyb 0.226
> 389 P1 A5ovca 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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Re: [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 A1ovca SKOV3hyb 0.184
+ 386 P1 A2ovca SKOV3hyb 0.229
+ 387 P1 A3ovca SKOV3hyb 0.214
+ 388 P1 A4ovca SKOV3hyb 0.226
+ 389 P1 A5ovca 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 A1SKOV3hyb0.190 SKOV3hyb 0.184
2 P1 A2SKOV3hyb0.210 SKOV3hyb 0.229
3 P1 A3SKOV3hyb0.205 SKOV3hyb 0.214
4 P1 A4SKOV3hyb0.206 SKOV3hyb 0.226
5 P1 A5SKOV3hyb0.184 SKOV3hyb 0.217
tst2$rlt1.diff <- rlt1.ovca - rlt1.Control
reshape() is reshaping the data based on plate.id * well.id combinations, so
the observations in Control and ovca should match on those two keys..
HTH,
Dennis
On Mon, Sep 27, 2010 at 12:47 PM, 1Rnwb wrote:
>
> Hello
>
> I have a data set like below:
>plate.id well.id Group HYB rlt1
> 1 P1 A1 Control SKOV3hyb 0.190
> 2 P1 A2 Control SKOV3hyb 0.210
> 3 P1 A3 Control SKOV3hyb 0.205
> 4 P1 A4 Control SKOV3hyb 0.206
> 5 P1 A5 Control SKOV3hyb 0.184
> 385 P1 A1ovca SKOV3hyb 0.184
> 386 P1 A2ovca SKOV3hyb 0.229
> 387 P1 A3ovca SKOV3hyb 0.214
> 388 P1 A4ovca SKOV3hyb 0.226
> 389 P1 A5ovca SKOV3hyb 0.217
> 390 P1 A6ovca SKOV3hyb 0.207
>
>
> each plate.id contains 384 readings for Group=="Control" and the same
> plate.id will contain 384 readings for Group=='ovca' to give a total of
> 768
> values for P1 and so on for other plate ID's. I have to take the subtract
> the values of rlt1 colum between the two groups based on Plate ID.
>
> currently I am using
> > newdat2$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 A1ovca SKOV3hyb 0.184 3.157895
> 386 P1 A2ovca SKOV3hyb 0.229 -9.047619
> 387 P1 A3ovca SKOV3hyb 0.214 -4.390244
> 388 P1 A4ovca SKOV3hyb 0.226 -9.708738
> 389 P1 A5ovca 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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Re: [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 A1ovca SKOV3hyb 0.184
386 P1 A2ovca SKOV3hyb 0.229
387 P1 A3ovca SKOV3hyb 0.214
388 P1 A4ovca SKOV3hyb 0.226
389 P1 A5ovca 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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[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 A1ovca SKOV3hyb 0.184 386 P1 A2ovca SKOV3hyb 0.229 387 P1 A3ovca SKOV3hyb 0.214 388 P1 A4ovca SKOV3hyb 0.226 389 P1 A5ovca SKOV3hyb 0.217 390 P1 A6ovca 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$diff<-(newdat2[1:5,5]-newdat2[6:10,5])/newdat2[1:5,5]*100 > newdat2 plate.id well.id Group HYB rlt1 diff 1 P1 A1 Control SKOV3hyb 0.190 3.157895 2 P1 A2 Control SKOV3hyb 0.210 -9.047619 3 P1 A3 Control SKOV3hyb 0.205 -4.390244 4 P1 A4 Control SKOV3hyb 0.206 -9.708738 5 P1 A5 Control SKOV3hyb 0.184 -17.934783 385 P1 A1ovca SKOV3hyb 0.184 3.157895 386 P1 A2ovca SKOV3hyb 0.229 -9.047619 387 P1 A3ovca SKOV3hyb 0.214 -4.390244 388 P1 A4ovca SKOV3hyb 0.226 -9.708738 389 P1 A5ovca SKOV3hyb 0.217 -17.934783 I have tried apply(newdat2, 1, function(x) tapply(x, plate.id, newdat2$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.
