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@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
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
________________________________________
L?hett?j?: Norman Pavelka [normanpavelka at gmail.com]
L?hetetty: 14. kes?kuuta 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@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
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
> ________________________________________
> L?hett?j?: Norman Pavelka [normanpavelka at gmail.com]
> L?hetetty: 14. kes?kuuta 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
Yes, that sorted it out! Thanks for the tip.
Cheers,
Olli
________________________________________
L?hett?j?: Norman Pavelka [normanpavelka at gmail.com]
L?hetetty: 15. kes?kuuta 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
> ________________________________________
> L?hett?j?: Norman Pavelka [normanpavelka at gmail.com]
> L?hetetty: 14. kes?kuuta 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
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
> ________________________________________
> L?hett?j?: Norman Pavelka [normanpavelka at gmail.com]
> L?hetetty: 15. kes?kuuta 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
>> ________________________________________
>> L?hett?j?: Norman Pavelka [normanpavelka at gmail.com]
>> L?hetetty: 14. kes?kuuta 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