[BioC] Problem with limma - psigamma?

[Gordon Smyth]

At 11:53 PM 22/03/2004, Matthew  Hannah wrote:
>I've just reinstalled everything, I used the compiled rw1090dev.exe
>win32 for install and it appears it does not contain the psigamma
>function (see below).

rw10910dev *does* include 'psigamma'. Tetragamma() is now a Deprecated 
function which as been replaced by psigamma(), hence I was forced to 
replace tetragamma() with psigamma() in limma. The limma code checks for 
which version of R it is getting so that limma will work in both R 1.8.1 
and R 1.9.0

>As for the error, is this psigamma new to the latest limma as previous 
>versions
>worked ok on the eBayes call. Any quick fix (other than dropping a limma 
>version),
>and should I contact someone about the win32 installer, or is someone on 
>this list
>in contact with the compiler?

Down-load the latest R 1.9.0, available from 
http://cran.at.r-project.org/bin/windows/base/rdevel.html. The print-out 
that you give below is not from R1.9.0alpha.

Gordon

>Cheers
>Matt
>
>
> > psigamma
>Error: Object "psigamma" not found
>
> > digamma
>function (x)
>.Internal(digamma(x))
><environment: namespace:base>
>
> >?Special
>Description:
>
>      Special mathematical functions related to the beta and gamma
>      functions.
>
>Usage:
>
>      beta(a, b)
>      lbeta(a, b)
>      gamma(x)
>      lgamma(x)
>      digamma(x)
>      trigamma(x)
>      tetragamma(x)
>      pentagamma(x)
>      choose(n, k)
>      lchoose(n, k)
>      factorial(x)
>      lfactorial(x)
>
>-----Original Message-----
>From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU]
>Sent: Montag, 22. März 2004 13:06
>To: Matthew Hannah
>Cc: bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] Problem with limma - psigamma?
>
>
> > Hi,
> >
> > I'm using R 1.9.0 and limma 1.5.6 (latest win32).
> >
> > I ran the following commands and got this error.
> >
> >>files <- dir(pattern="*.spot")
> >>RG <- read.maimages(files, source="spot")
> >>RG$genes <- readGAL("GAL.tbl")
> >>RG$printer <- getLayout(RG$genes)
> >>MA <- normalizeWithinArrays(RG)
> >>MA <- normalizeBetweenArrays(MA)
> >>fit <- lmFit(MA, design=c(-1,1,-1))
> >>fit <- eBayes(fit)> version
>          _
> > Error in tetraGamma(y) : couldn't find function "psigamma"
> >
> > Anyone able to help? Am I doing something wrong?
>
>Are you sure that you're using R 1.9.0?  psigamma() is a new function in R
>1.9.0:
>
> > psigamma
>function (x, deriv = 0)
>.Internal(psigamma(x, deriv))
><environment: namespace:base>
>
> > version
>platform i386-pc-mingw32
>arch     i386
>os       mingw32
>system   i386, mingw32
>status   alpha
>major    1
>minor    9.0
>year     2004
>month    03
>day      17
>language R
>
>Gordon
>
> > Thanks
> > Matt