[BioC] Problem with limma - psigamma?
Martin Maechler
maechler at stat.math.ethz.ch
Tue Mar 23 10:40:57 CET 2004
>>>>> "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
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