Hi,
I downloaded data on the GEO web site and now, I try to analyze
them
with R 2.0.1 for windows XP but in this dataset, there is a lot of
negative
values. So when I normalyze with log2 transformation, R produced NaNs.
I
understand why but after, when I want to calculate p-value with the
parametric t test, R can't. I tried to write 0 where there is a
negative
value : R calculate p-value and q-value but all of q-value are at 1.
Is there someone to help me.
Thanks a lot
Hi Guillaume,
some image processing / background correction methods produce negative
estimates. In many cases, the "vsn" method from the package of the
same
name can deal with this. It uses the "glog" transformation, and
glog(x)
is similar to log(x+x0) with appropriate choice of x0. Please read the
vignette carefully and use the diagnostic plot "meanSdPlot" to see
whether it makes sense on your data.
While true gene abundances are obviously always >=0, it can make sense
to have negative estimates if you have an error model that includes a
Normally (or similar) distributed additive noise term. Because if Y is
the observation, x is the true value, and eps the noise,
Y = x + eps
will be negative half of the times if x=0.
Bw
Wolfgang
Deplaine wrote:
> Hi,
>
> I downloaded data on the GEO web site and now, I try to analyze
them
> with R 2.0.1 for windows XP but in this dataset, there is a lot of
> negative values. So when I normalyze with log2 transformation, R
> produced NaNs. I understand why but after, when I want to calculate
> p-value with the parametric t test, R can't. I tried to write 0
where
> there is a negative value : R calculate p-value and q-value but all
of
> q-value are at 1.
>
> Is there someone to help me.
> Thanks a lot
>
-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax: +44 1223 494486
Http: www.ebi.ac.uk/huber
Dear all
I am trying to build an R package in Windows 2000 that I want to
upload in
Bioconductor. I have created the man and R folders with the
appropriate
files inside and I use the command Rcmd check C:\...\roots to check
whether
the package works properly, but the following problem appears:
-------------------------------------------------------
* using log directory 'C:/Program Files/R/rw2001/bin/roots.Rcheck'
* checking for file 'roots/DESCRIPTION' ... OK
* checking if this is a source package ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking package dependencies ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... WARNING
Error in .try_quietly({ : Error: Unable to load R code in package
'roots'
Execution halted
See section 'Generic functions and methods' of the 'Writing R
Extensions'
manual.
* checking replacement functions ... WARNING
Error in .try_quietly({ : Error: Unable to load R code in package
'roots'
Execution halted
In R, the argument of a replacement function which corresponds to the
right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Error in .try_quietly({ : Error: Unable to load R code in package
'roots'
Execution halted
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking Rd files ... OK
* checking for missing documentation entries ... ERROR
Error in .try_quietly({ : Error: Unable to load R code in package
'roots'
--------------------------------------------------------
Could someone tell how to correct for the warnings, please?
Regards,
Makis
----------------------
E Motakis, Mathematics
E.Motakis at bristol.ac.uk
On 6/21/05, E Motakis, Mathematics <e.motakis at="" bristol.ac.uk=""> wrote:
> Dear all
>
> I am trying to build an R package in Windows 2000 that I want to
upload in
> Bioconductor. I have created the man and R folders with the
appropriate
> files inside and I use the command Rcmd check C:\...\roots to check
whether
> the package works properly, but the following problem appears:
>
> -------------------------------------------------------
> * using log directory 'C:/Program Files/R/rw2001/bin/roots.Rcheck'
> * checking for file 'roots/DESCRIPTION' ... OK
> * checking if this is a source package ... OK
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking package dependencies ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking R files for syntax errors ... OK
> * checking R files for library.dynam ... OK
> * checking S3 generic/method consistency ... WARNING
> Error in .try_quietly({ : Error: Unable to load R code in package
'roots'
> Execution halted
> See section 'Generic functions and methods' of the 'Writing R
Extensions'
> manual.
> * checking replacement functions ... WARNING
> Error in .try_quietly({ : Error: Unable to load R code in package
'roots'
> Execution halted
> In R, the argument of a replacement function which corresponds to
the right
> hand side must be named 'value'.
> * checking foreign function calls ... WARNING
> Error in .try_quietly({ : Error: Unable to load R code in package
'roots'
> Execution halted
> See section 'System and foreign language interfaces' of the 'Writing
R
> Extensions' manual.
> * checking Rd files ... OK
> * checking for missing documentation entries ... ERROR
> Error in .try_quietly({ : Error: Unable to load R code in package
'roots'
> --------------------------------------------------------
>
> Could someone tell how to correct for the warnings, please?
>
> Regards,
> Makis
Well the warnings indicate that there is a syntax error in your R
source code. You will need to source each of the R files in your
package separately to determine where the problem is. It can be
something as trivial as a missing or an extra comma, which is my
typical error.
I generally do something like
base <- "roots/R" # change to the proper directory path
nms <- list.files(base, pattern = "\.R$")
for (nm in nms) {print(nm);source(file.path(base,nm))}
That should produce an error message from one of the calls to source()
and it will occur in the file whose name has just been printed.
