[BioC] FW: plgem

[Norman Pavelka]

I'm glad it worked. Hope the results are interesting, too! :-)

Cheers,
Norman

On Fri, Jun 15, 2012 at 5:54 PM, Olli Kannaste <ojkann at utu.fi> wrote:
> 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