[BioC] Fwd: FW: plgem

[Norman Pavelka]

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