R help - Jun 2010 - help for reshape function

hi, everyone:

i have a question on the reshape function. i have the following dataset :
gene   tissue        patient1 patient2 patient3.............
_________________________________________________
gene1   breast         10       20       50
gene2   breast         20       40       60
gene3   breast         100      200      300

which i hope to convert to the following format:

gene patientID value  gene1
-----------------------------
gene1   1       10    10
gene1   2       20    20
gene1   3       50    100
gene2   1       20    10
gene2   2       40    20
gene2   3       60    100

the column "gene" is required and column "tissue" is not
needed. I use the
following syntax to perform this task:

tdata<- reshape(data,
varying=names(data)[-c(1,2)],direction="long", timevar
="label",v.names="value",time=names(data)[-c(1,2)]);

however, i lose the column "gene" in the resulting tranposed dataset.
I did
my best to go through the help doc for reshape. however, I am frustrated
that the examples used in the help doc is kind o hard to follow to me. Can
anyone help me modify the code to keep the column "gene" in the
resulting
table? 

Any constructive suggestion is welcome. 
thanks


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Try this:

 reshape(x, direction = 'long', varying = list(3:5), timevar =
"gene",
v.names = "value")

On Thu, Jun 17, 2010 at 3:22 PM, xin wei <xinwei@stat.psu.edu> wrote:
>
> hi, everyone:
>
> i have a question on the reshape function. i have the following dataset :
> gene   tissue        patient1 patient2 patient3.............
> _________________________________________________
> gene1   breast         10       20       50
> gene2   breast         20       40       60
> gene3   breast         100      200      300
>
> which i hope to convert to the following format:
>
> gene patientID value  gene1
> -----------------------------
> gene1   1       10    10
> gene1   2       20    20
> gene1   3       50    100
> gene2   1       20    10
> gene2   2       40    20
> gene2   3       60    100
>
> the column "gene" is required and column "tissue" is
not needed. I use the
> following syntax to perform this task:
>
> tdata<- reshape(data,
varying=names(data)[-c(1,2)],direction="long",
> timevar
> ="label",v.names="value",time=names(data)[-c(1,2)]);
>
> however, i lose the column "gene" in the resulting tranposed
dataset. I did
> my best to go through the help doc for reshape. however, I am frustrated
> that the examples used in the help doc is kind o hard to follow to me. Can
> anyone help me modify the code to keep the column "gene" in the
resulting
> table?
>
> Any constructive suggestion is welcome.
> thanks
>
>
> --
> View this message in context:
>
http://r.789695.n4.nabble.com/help-for-reshape-function-tp2259286p2259286.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.
>


-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O

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I am afraid that your solution is not solving the problem. it seems that
timevar="gene" just create the followings:

GENE        SAMPLE   value id
1.1        1 Kidney 3.69351  1
2.1        1 Kidney 5.42710  2
3.1        1 Kidney 5.26883  3
4.1        1 Kidney 2.88098  4
5.1        1 Kidney 4.68519  5
6.1        1 Kidney 5.92774  6 ]

here the "gene" is just a empty column. I also lost the column that is
supposed to store the header name of transposed variables in my target
table.

more suggests?

thanks
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