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$genes)
>MA <- normalizeWithinArrays(RG)
>MA <- normalizeBetweenArrays(MA)
>fit <- lmFit(MA, design=c(-1,1,-1))
>fit <- eBayes(fit)
Error in tetraGamma(y) : couldn't find function "psigamma"
Anyone able to help? Am I doing something wrong?
Thanks
Matt
> Hi,
>
> I'm using R 1.9.0 and limma 1.5.6 (latest win32).
>
> I ran the following commands and got this error.
>
>>files <- dir(pattern="*.spot")
>>RG <- read.maimages(files, source="spot")
>>RG$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
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@wehi.EDU.AU]
Sent: Montag, 22. M?rz 2004 13:06
To: Matthew Hannah
Cc: bioconductor@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
>>>>> "Matthew" == Matthew Hannah <hannah@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@wehi.EDU.AU] Sent: Montag, 22. M?rz
Matthew> 2004 13:06 To: Matthew Hannah Cc:
Matthew> bioconductor@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
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@wehi.EDU.AU]
>Sent: Montag, 22. M?rz 2004 13:06
>To: Matthew Hannah
>Cc: bioconductor@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
Thanks very much for that link, the printout I gave was from the R1.9
I
downloaded on 6/02/04 from the link for downloading Rdevel from the
bioCdevel page, which I assumed was the latest version.
http://www.bioconductor.org/downloadingRdevel.html
This link to the download no longer functions and I have been looking
to
see if there was a newer version but (maybe I missed it) there is no
obvious link from the R homepage, such as from the developer page or
the
cran download page.
>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
It seems I was unlucky in having the only version of R which didn't
work
with limma as it was recognised as 1.9, but as it was prior to the
alpha
release it didn't have psigamma.
>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.
Thanks, for sorting this out for me, and pointing me in the right
direction
for keeping Rdevel up to date.
Matt
