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burak kutlu | 1 Oct 2006 06:41
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justPlier outputs negative values

Hi 

I am analyzing affy data with 'justPlier()' and there are some negative values
9586 out of 427536  values

 There are some as low as 0.0002 on log2 scale(whatever the default scale of values calculated by justPlier)

The PLIER documentation mentions addition of 16 (or 32) to the low values. Is 'justPlier' supposed to that? 

Is this a bug?

Many thanks
-burak

> sessionInfo()
Version 2.3.1 (2006-06-01)
i686-pc-linux-gnu

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"

other attached packages:
   plier     affy   affyio  Biobase
 "1.4.0" "1.10.0"  "1.0.0" "1.10.0"

 		
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marco fabbri | 2 Oct 2006 11:25
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font size problem

I got an error for font size. I work with suse 10 and I have those package
installed:
xorg-x11-fonts-100dpi-6.8.2-100.i586.rpm
xorg-x11-fonts-75dpi-6.8.2-100.i586.rpm

>plotPCA(esetPTX3,groups=rep(1:4,each=3),groupnames=c("Ctrl","Con","P3","CP"))
Error in title(...) : X11 font at size 14 could not be loaded

Any suggestion?

Thanx Mcrco
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Istituto Clinico Humanitas
via Manzoni, 52
20089 Rozzano (Mi)
Tel. 028224 5152
Fax 028224 5101

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Gaj Stan (BIGCAT | 2 Oct 2006 15:17
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Single Channel Approach for Agilent Arrays

Dear BioConductor-user,

I've recently tested out Chapter 9 in the Limma user documentation concerning applying single channel
approach on Agilent arrays. My experimental setup consists of two different (pooled) food
interventions in dye flip using the same control sample (n=4 - For each experiment, 1 array + dye-flip). I
assume that my ultimate single-channel design matrix would look like this

	fControl	fFood1		fFood2
(1)	1	0	0
(2)	0	1	0
(3)	0	1	0
(4)	1	0	0
(5)	1	0	0
(6)	0	0	1
(7)	0	0	1
(8)	1	0	0

Where:
Food1_vs_Control.Cy3 (1)
Food1_vs_Control.Cy5 (2)
Control_vs_Food1.Cy3 (3)
Control_vs_Food1.Cy5 (4)
Food2_vs_Control.Cy3 (5)
Food2_vs_Control.Cy5 (6)
Control_vs_Food2.Cy3 (7)
Control_vs_Food2.Cy5 (8)

Question 1: Am I missing any information here? Because if I do this as suggested in the manual, I get a matrix
with some extra (and empty) attributes such as assign (1,1,1), contrasts (NULL) and contrasts$f
("contr.treatment"). Are these attributes necessary for further steps?
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Alvord, Greg (DMS) [Contr] | 2 Oct 2006 16:35

Re: justPlier outputs negative values

Hi Burak - 

I'm a newbie with Bioconductor and R, so I don't know whether this helps
or hurts.  

I executed 'justPlier()' on several data sets on which I was somewhat
familiar.  I compared results with those I obtained using mas5 and rma.
I am not qualified to say whether there are bugs in the justPlier
program, but I concluded that I did not trust the results.  Diagnostic
plots, MA-plots, etc., indicated bizarre results.  It may be that I have
executed the program incorrectly, perhaps choosing inadequate options,
etc.  However, with limited time, I chose, temporarily, to NOT use the
justPlier algorithm.  

Sorry to sound so pessimistic.  Perhaps some other members on the list
can provide more assistance.

	Greg

W. Gregory Alvord, Ph.D.
Director, Statistical Consulting Services
Computer and Statistical Services
National Cancer Institute at Frederick
Post Office Box B 
Frederick, MD 21702-1201
Phone: 301.846.5101
Facsimile: 301.846.6196
E-Mail gwa@...

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Wonjong Moon | 1 Oct 2006 01:30

Error message: no package 'file5f906952' was found

Where can I get package 'file5f906952'?

Here are examples when I had error message 'no package 'file5f906952'
was found'

> utils:::menuInstallLocal()
package 'ALLMLL' successfully unpacked and MD5 sums checked
updating HTML package descriptions
Warning message:
no package 'file5f906952' was found in: packageDescription(i, lib.loc =
lib, field = "Title", encoding = "UTF-8") 

> help.search("somefunc")
Error in help.search("somefunc") : could not find package 'file5f906952'

Thank you.

Wonjong

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Ganiraju Manyam | 2 Oct 2006 18:02
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Regarding error while normalizing using "loess" method

hi all,

I am Ganiraju, a new member of the group. (and currently using the affy
package)

I m trying to use "loess" method in expresso function to normalize the data.

While running Im getting an error: "non-numeric matrix extent"

I didnt really understand whether is some problem with ReadAffy(), or
functinoality of "loess", whether it can be used on all kinds of data or
not.

Also, Im runnig sort of memory. Is there any other way to create virtual
memory other than using "memory.limit."

Thanks in advance,
Ganiraju

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James W. MacDonald | 2 Oct 2006 18:57
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Re: Regarding error while normalizing using "loess" method

Hi Ganiraju,

Ganiraju Manyam wrote:
> hi all,
> 
> I am Ganiraju, a new member of the group. (and currently using the affy
> package)
> 
> I m trying to use "loess" method in expresso function to normalize the data.
> 
> While running Im getting an error: "non-numeric matrix extent"
> 
> I didnt really understand whether is some problem with ReadAffy(), or
> functinoality of "loess", whether it can be used on all kinds of data or
> not.

You really need to give more information than this. At a minimum, you 
need to give the commands you ran along with the results (i.e., copying 
and pasting from within R). You should also give the results that you 
get when you run sessionInfo() after loading all the packages you are 
using here.

> 
> Also, Im runnig sort of memory. Is there any other way to create virtual
> memory other than using "memory.limit."

Assuming you are on windows, as AFAIK, this command doesn't exist for 
*nix or MacOS, the short answer is no. You can set the command line flag 
--max-mem-size in the shortcut you use to launch R, setting this value 
to the amount of RAM you have. If you still run out of memory, the next
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James W. MacDonald | 2 Oct 2006 19:20
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Re: Error message: no package 'file5f906952' was found

Wonjong Moon wrote:
> Where can I get package 'file5f906952'?
> 
> Here are examples when I had error message 'no package 'file5f906952'
> was found'
> 
> 
>>utils:::menuInstallLocal()
> 
> package 'ALLMLL' successfully unpacked and MD5 sums checked
> updating HTML package descriptions
> Warning message:
> no package 'file5f906952' was found in: packageDescription(i, lib.loc =
> lib, field = "Title", encoding = "UTF-8")

I think we will probably need more help here. What version of ALLMLL, R, 
  at the very least.

On R-2.4.0RC, I get the following result:

 > biocLite("ALLMLL")
Running getBioC version 0.1.8 with R version 2.4.0
Running biocinstall version 1.9.6 with R version 2.4.0 (under development)
Your version of R requires version 1.9 of Bioconductor (under 
development too).
trying URL 
'http://bioconductor.org/packages/1.9/data/experiment/bin/windows/contrib/2.4/ALLMLL_1.1.2.zip'
Content type 'application/zip' length 39343027 bytes
opened URL
downloaded 38420Kb
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James W. MacDonald | 2 Oct 2006 19:29
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Re: Question about "kidpack" installation

Hi Wang Shengjun,

王胜军 wrote:
> Dear sir,
> 
> 	When I install the "kidpack" package using kidpack-1.2.1.zip,
> following information is displayed.
> 
>     > utils:::menuInstallLocal()
>     files R/all.rda are missing
>     updating HTML package descriptions
> 
>    Would you like tell me what's the trouble?  
>    By the way, the OS is XP, and the version of R is 2.3.1.

That package appears to be busted - I get the same result. However, this
one works for me:

http://bioconductor.org/packages/1.9/data/experiment/bin/windows/contrib/2.4/kidpack_1.3.3.zip

HTH,

Jim

> 
>    Thanks.
> 
> ��������   Wang Shengjun
>                   wsj <at> fimmu.com
> ����������2006-09-30
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Martin Morgan | 2 Oct 2006 19:57

Re: Question about "kidpack" installation

"王胜军" <wsj@...> writes:

There is a problem with the kidpack-1.2.1.zip file; it has been
replaced with kidpack-1.2.2.zip. Thank you for the report.

> Dear sir,
>
> 	When I install the "kidpack" package using kidpack-1.2.1.zip,
> following information is displayed.
>
>     > utils:::menuInstallLocal()
>     files R/all.rda are missing
>     updating HTML package descriptions
>
>    Would you like tell me what's the trouble?  
>    By the way, the OS is XP, and the version of R is 2.3.1.
>
>    Thanks.
>
> 　　　　　　　　   Wang Shengjun
>                   wsj@...
> 　　　　　　　　　　2006-09-30
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@...
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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