[BioC] FW: plgem

[Olli Kannaste]

Yes, that sorted it out! Thanks for the tip.

Cheers,
Olli
________________________________________
Lähettäjä: Norman Pavelka [normanpavelka at gmail.com]
Lähetetty: 15. kesäkuuta 2012 6:04
Vastaanottaja: Olli Kannaste
Cc: bioconductor at r-project.org
Aihe: Re: FW: plgem

Hi Olli,

As I suspected, you are using a very old version of R and Bioconductor
(2008). Try downloading the latest version of R and re-install the
latest plgem package by typing:

  source("http://bioconductor.org/biocLite.R")
  biocLite("plgem")

Let me know if this solves the problem.

Cheers,
Norman

On Thu, Jun 14, 2012 at 4:52 PM, Olli Kannaste <ojkann at utu.fi> wrote:
> Hi Norman,
>
> Sure thing. Here is the output:
>
> R version 2.7.2 (2008-08-25)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] plgem_1.12.0  MASS_7.2-44   Biobase_2.0.1
>
> --
>
> Thanks,
> Olli
> ________________________________________
> Lähettäjä: Norman Pavelka [normanpavelka at gmail.com]
> Lähetetty: 14. kesäkuuta 2012 4:35
> Vastaanottaja: Olli Kannaste
> Cc: bioconductor at r-project.org
> Aihe: Fwd: FW: plgem
>
> Dear Olli,
>
> Thanks for your email and your continued interest in plgem. From your
> error message it looks like there might be a version problem. Could
> you please send me the output of sessionInfo() ?
> I am also copying the Bioconductor mailing list, so the thread gets archived.
>
> Cheers,
> Norman
>
> -----Original Message-----
> From: Olli Kannaste [mailto:ojkann at utu.fi]
> Sent: Wednesday, 13 June, 2012 9:07 PM
> To: Norman Pavelka (SIgN)
> Subject: plgem
>
> Hi Norman,
>
> I approached you about 2.5 years ago regarding problems i was having
> with the plgem analysis. You were kind enough to provide me an R
> script, which automated the analysis. That worked fine and helped me a
> great deal. I am now trying plgem again using the script with some
> other data, and having some difficulties... I'm working on a different
> computer now and have installed the latest version of plgem. My guess
> is that for some reason the script is not working properly with the
> new plgem version. It lets me input my parameters and specify data
> files but fails to proceed right after that, generating the following
> error message:
>
> Error in run.plgem(get(expressionSetName), signLev = pVal, rank = 100,  :
>  unused argument(s) (trimAllZeroRows = TRUE, zeroMeanOrSD = "replace")
>
> Could you perhaps help me out with this one? I'm attaching the script
> and my input files in the message.
>
> Best regards,
> Olli