[BioC] Problem with limma - psigamma?

[Martin Maechler]

>>>>> "Matthew" == Matthew Hannah <Hannah at mpimp-golm.mpg.de>
>>>>>     on Mon, 22 Mar 2004 13:53:11 +0100 writes:

    Matthew> I've just reinstalled everything, I used the
    Matthew> compiled rw1090dev.exe win32 for install and it
    Matthew> appears it does not contain the psigamma function
    Matthew> (see below).

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

    Matthew> Cheers Matt

The code and help(Special) you show here
is definitely from a very old version of "R-devel" (aka "R 1.9.0
(unstable)") or R an version <= 1.8.x {as Gordon rightly says below}.

All "R-1.9.0 alpha" and "beta" versions have had the psigamma()
and deprecated the tetra* and penta*gamma functions.

I happen to know this because I did the implementation.
Martin Maechler


    >> psigamma
    Matthew> Error: Object "psigamma" not found

    >> digamma
    Matthew> function (x) .Internal(digamma(x)) <environment:
    Matthew> namespace:base>

    >> ?Special
    Matthew> Description:

    Matthew>      Special mathematical functions related to the
    Matthew> beta and gamma functions.

    Matthew> Usage:

    Matthew>      beta(a, b) lbeta(a, b) gamma(x) lgamma(x)
    Matthew> digamma(x) trigamma(x) tetragamma(x) pentagamma(x)
    Matthew> choose(n, k) lchoose(n, k) factorial(x)
    Matthew> lfactorial(x)

    Matthew> -----Original Message----- From: Gordon K Smyth
    Matthew> [mailto:smyth at wehi.EDU.AU] Sent: Montag, 22. März
    Matthew> 2004 13:06 To: Matthew Hannah Cc:
    Matthew> bioconductor at stat.math.ethz.ch Subject: Re: [BioC]
    Matthew> 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
    Matthew>          _
    >> Error in tetraGamma(y) : couldn't find function
    >> "psigamma"
    >> 
    >> Anyone able to help? Am I doing something wrong?

    Matthew> Are you sure that you're using R 1.9.0?  psigamma()
    Matthew> is a new function in R 1.9.0:

    >> psigamma
    Matthew> function (x, deriv = 0) .Internal(psigamma(x,
    Matthew> deriv)) <environment: namespace:base>

    >> version
    Matthew> platform i386-pc-mingw32 arch i386 os mingw32
    Matthew> system i386, mingw32 status alpha major 1 minor 9.0
    Matthew> year 2004 month 03 day 17 language R

    Matthew> Gordon

    >> Thanks Matt