[BioC] Problem with limma - psigamma?

[Matthew Hannah]

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).

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?

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