Sean Davis | 10 Dec 13:50 2004
Picon

Re: Limma FDR question

See ?p.adjust for specifics.  However, in a particular case, if one has 
100 genes with fdr less than 0.05, then 5 out of that 100 are expected 
to be false positive.  In other words, for any given fdr cutoff x, if 
there are N genes with fdr<x, then x*N genes are expected to be false 
discoveries.

Sean

On Dec 10, 2004, at 7:21 AM, M PEREZ wrote:

>
> Hi all,
>
> I was wondering how the p-value correction using fdr works.
>
> The following Limma package's command " topTable(fit,number=100, 
> adjust="fdr")" corrects the p-values but I don't know which is the 
> percent of false positive we can expect using  this correction. Is the 
> FDR fixing at one pre-determined value, e.g.  5 %?
>
> Thank you in advance
>
> Best,
>
> Manuel
>
>
> 		
> ---------------------------------
>
(Continue reading)

Ramon Diaz-Uriarte | 10 Dec 14:00 2004
Picon

Re: Limma FDR question

Dear Manuel,

You are selecting the top-ranked number genes, ordered using the "sort.by" 
option; the p-value you are seeing is the fdr-adjusted p-value, so no, no 
pre-determined cut-off has been selected. Some explanation is provided in the 
help for p.adjust; here you also have an extensive list of references. You 
might want to add to that the documentation of the multtest package which 
provides a quick overview of multiple testing issues, including the 
definition of adjusted p-value according to FDR.

Best,

R.

On Friday 10 December 2004 13:21, M PEREZ wrote:
> Hi all,
>
> I was wondering how the p-value correction using fdr works.
>
> The following Limma package’s command “ topTable(fit,number=100,
> adjust="fdr")” corrects the p-values but I don’t know which is the percent
> of false positive we can expect using  this correction. Is the FDR fixing
> at one pre-determined value, e.g.  5 %?
>
> Thank you in advance
>
> Best,
>
> Manuel
>
(Continue reading)

Anja.von.Heydebreck | 10 Dec 14:41 2004
Picon

normalizaton between studies

Dear Arne,

> The problem is that the studies have quite different intensity
> distributions of the PMs). I've some doubts that RMA or VSN are
> appropiate normalization methods for this problem. Forcing all
> distributions to be the same may buffer the very strong study
> effect but may also erase some of the tiny (but significant)
> differences due to dose.

Actually, VSN does not enforce intensity distributions to be the
same. The normalization in VSN amounts to an affine-linear mapping
of the intensities of each chip, that is, for each chip only a
multiplicative/scaling factor and an additive offset are estimated
from the data.

Best regards,
Anja

--
Dr. Anja von Heydebreck
Global Technologies
Bio- and Chemoinformatics
Merck KGaA
64271 Darmstadt
Germany
Phone: +49-6151-723235, Fax: +49-6151-723329
Email: anja.von.heydebreck@...
http://www.merck.de
Glynn, Earl | 10 Dec 19:21 2004

Need better quality control for reliable installation of bioconductor packages?

Under Windows I just downloaded the new 2.0.1 version of R and installed
all the packages:

	Packages | Install package(s) from CRAN ... 

I select all the packages for installation and that worked fine.  This
took about an hour.

So with the new version of R, I thought I'd re-install all the
Bioconductor packages. Like several times in the past, when I try to
install all the Bioconductor packages I encounter problems:

	Packages | Install package(s) from Bioconductor ...

I select all the packages for installation.  The download take a long
time but then the installation of packages fails.  I wish the name of
the temporary download directory was displayed earlier to make it easier
to find.  But I found the Bioconductor ZIP files and then tried Packages
| Install Package(s) from local zip files ...

Why is the installation of so many Bioconductor packages failing?

For example:

	>
install.packages(choose.files('',filters=Filters[c('zip','All'),]),
.libPaths()[1], CRAN = NULL)
	Error in file(file, "r") : unable to open connection
	In addition: Warning messages: 
	1: error 1 in extracting from zip file 
(Continue reading)

Robert Gentleman | 10 Dec 20:17 2004

Re: Need better quality control for reliable installation of bioconductor packages?


On Dec 10, 2004, at 10:21 AM, Glynn, Earl wrote:

> Under Windows I just downloaded the new 2.0.1 version of R and  
> installed
> all the packages:
>
> 	Packages | Install package(s) from CRAN ...
>
> I select all the packages for installation and that worked fine.  This
> took about an hour.
>
> So with the new version of R, I thought I'd re-install all the
> Bioconductor packages. Like several times in the past, when I try to
> install all the Bioconductor packages I encounter problems:
>
> 	Packages | Install package(s) from Bioconductor ...
>
> I select all the packages for installation.  The download take a long
> time but then the installation of packages fails.  I wish the name of
> the temporary download directory was displayed earlier to make it  
> easier
> to find.  But I found the Bioconductor ZIP files and then tried  
> Packages
> | Install Package(s) from local zip files ...
>
> Why is the installation of so many Bioconductor packages failing?
>
> For example:
>
(Continue reading)

Rafael A. Irizarry | 10 Dec 20:58 2004

automatic data package maker

hi!

is there a utility to automatically create a data package? 

if not, im making one cause i have tons of rdas lying around that i want 
to load using library instead of load.

it will take as input the location of an rda, location to save the 
package, package title, package author, and text describing the data 
(for the Rd file) and create a package for that data set.

any auxiliary untility that i should be using?

-r
Tomas Radivoyevitch | 10 Dec 22:36 2004
Picon

Re: automatic data package maker

Doing this manually has been taking me 1 to 2 hours a pop.

Related to your question, a few weeks ago I tried to post the two questions 
below. Regarding the second of these and your question, perhaps the solution 
is to simply get everyone into the habit of making R data packages and 
sending them up to Bioconductor. It would be nice if manuscripts started 
coming with R scripts as "additional files" so that figures could be 
reproduced, and having the corresponding datasets up at bioconductor as R 
packages would certainly help.

Q1:   Does anyone have an automatic approach to grabbing GEO soft files and 
making esets out of them?

Q2:   Regarding R Data packages as an alternative to grabbing things from 
GEO, can anyone explain why there are so few (if any) GEO datasets also up 
at Bioconductor? I'm wondering if there's some sort of legal hindrance going 
on, or if it's just the leg work that's missing.

----- Original Message ----- 
From: "Rafael A. Irizarry" <ririzarr@...>
To: <bioconductor@...>
Sent: Friday, December 10, 2004 2:58 PM
Subject: [BioC] automatic data package maker

> hi!
>
> is there a utility to automatically create a data package?
>
> if not, im making one cause i have tons of rdas lying around that i want
> to load using library instead of load.
(Continue reading)

Robert Gentleman | 10 Dec 23:55 2004

Re: automatic data package maker


On Dec 10, 2004, at 1:36 PM, Tomas Radivoyevitch wrote:

> Doing this manually has been taking me 1 to 2 hours a pop.
>
> Related to your question, a few weeks ago I tried to post the two  
> questions below. Regarding the second of these and your question,  
> perhaps the solution is to simply get everyone into the habit of  
> making R data packages and sending them up to Bioconductor. It would  
> be nice if manuscripts started coming with R scripts as "additional  
> files" so that figures could be reproduced, and having the  
> corresponding datasets up at bioconductor as R packages would  
> certainly help.
>
> Q1:   Does anyone have an automatic approach to grabbing GEO soft  
> files and making esets out of them?

   I think not, but things like readGEOAnn could be used for such  
purposes. If they do not fit your requirements please let us know as we  
would happily take patches/improvements (on these and virtually any  
other functions).

>
> Q2:   Regarding R Data packages as an alternative to grabbing things  
> from GEO, can anyone explain why there are so few (if any) GEO  
> datasets also up at Bioconductor? I'm wondering if there's some sort  
> of legal hindrance going on, or if it's just the leg work that's  
> missing.
>

(Continue reading)

Glynn, Earl | 11 Dec 00:33 2004

RE: Need better quality control for reliable installation of bioconductor packages?

I'm using Windows 2000 on one machine and Windows XP on another machine.
The XP machine is not attached to the network.  I did a clean install of
the new R 2.0.1 on the network machine.  I downloaded the files once,
burned a CD and used them to install R and Bioconductor on the XP PC not
connected to the network.  This went flawlessly for R, but not for
Bioconductor.

>   But you have not shown us what commands you are using?

But I believe I have.  My description said I was using the Windows
interface (from the Rgui.exe program from R 2.0.1) and I selected:

R:  Packages | Install package(s) from CRAN ... | <select all packages>
Bioconductor:  Packages | Install package(s) from Bioconductor ... |
<select all packages>

One selects all the packages by clicking and dragging over the desired
files. One then presses OK using the Rgui.exe interface.  R installed
everything and the complete installation worked fine as usual.  

My experience with Bioconductor installation is that there are usually
several failures installing everything without messages that explain
why. 

>   You can (and possibly should) use the reposTools library 
> and the tools  
> that we have built for dealing with the package dependencies 
> that exist  
> in and between many Bioconductor packages.

(Continue reading)

Gordon K Smyth | 11 Dec 15:43 2004
Picon
Picon

Need better quality control for reliable installation of bioconductor packages?

Robert Gentleman rgentlem@... wrote
>On Dec 10, 2004, at 10:21 AM, Glynn, Earl wrote:
>> Under Windows I just downloaded the new 2.0.1 version of R and
>> installed
>> all the packages:
>>
>> 	Packages | Install package(s) from CRAN ...
>>
>> I select all the packages for installation and that worked fine.  This
>> took about an hour.
>>
>> So with the new version of R, I thought I'd re-install all the
>> Bioconductor packages. Like several times in the past, when I try to
>> install all the Bioconductor packages I encounter problems:
>>
>> 	Packages | Install package(s) from Bioconductor ...
>>
>> I select all the packages for installation.  The download take a long
>> time but then the installation of packages fails.  I wish the name of
>> the temporary download directory was displayed earlier to make it
>> easier
>> to find.  But I found the Bioconductor ZIP files and then tried
>> Packages
>> | Install Package(s) from local zip files ...
>>
>> Why is the installation of so many Bioconductor packages failing?
>>
>> For example:
>>
>
(Continue reading)


Gmane