Re: [R] samr result

2008-06-11 Thread Eleni Christodoulou 
Yes, here it is:
samr.obj-samr(data,resp.type=Two class unpaired, nperms=100,
center.arrays=T)

where *data *is a matrix of microarray gene expressions with genes as rows
and tissues as columns. With putting *center.arrays=T *the *data* matrix is
normalized such as each column has median=0. I would like to retrieve the
new normalized matrix, but it seems that it is not returned by *samr.* If
you have any idea on how I can find this transformed matrix I would be glad
to hear that!

Thanks again,
E.



On Tue, Jun 10, 2008 at 11:30 PM, Richardson, Patrick 
[EMAIL PROTECTED] wrote:

 Could you post your code so we can see what you are trying to do?

 Thanks,

 Patrick

 
 From: [EMAIL PROTECTED] [EMAIL PROTECTED] On
 Behalf Of Eleni Christodoulou [EMAIL PROTECTED]
 Sent: Tuesday, June 10, 2008 11:20 AM
 To: r-help@r-project.org
 Subject: [R] samr result

 Hello list!

 I have a proble trying to perform a SAM analysis using the function samr
 from the samr package. I have put the option *center.arrays=TRUE *in order
 to scale all the experiments to median=0. I would like to retrieved the
 scaled data but it seems that samr does not return it...Does anyone have
 any
 idea on this?

 Thanks a lot!!!
 E.

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[R] samr result

2008-06-10 Thread Eleni Christodoulou 
Hello list!

I have a proble trying to perform a SAM analysis using the function samr
from the samr package. I have put the option *center.arrays=TRUE *in order
to scale all the experiments to median=0. I would like to retrieved the
scaled data but it seems that samr does not return it...Does anyone have any
idea on this?

Thanks a lot!!!
E.

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] samr result

2008-06-10 Thread Richardson, Patrick 
Could you post your code so we can see what you are trying to do?

Thanks,

Patrick


From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Eleni Christodoulou 
[EMAIL PROTECTED]
Sent: Tuesday, June 10, 2008 11:20 AM
To: r-help@r-project.org
Subject: [R] samr result

Hello list!

I have a proble trying to perform a SAM analysis using the function samr
from the samr package. I have put the option *center.arrays=TRUE *in order
to scale all the experiments to median=0. I would like to retrieved the
scaled data but it seems that samr does not return it...Does anyone have any
idea on this?

Thanks a lot!!!
E.

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
This email message, including any attachments, is for th...{{dropped:6}}

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.