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Gordon Smyth | 1 Apr 2005 01:07
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Re: MAPlot

At 12:29 AM 1/04/2005, Mohammad Esad-Djou wrote:
>Hello,
>
>I would like Compare 1. experiment with set of experiments 2 to 7 and wrote:
>
>library(limma)
>plotMA(data.exprs, array=1, xlab = "A", ylab="M", main="Gene Signal M/A Plot")
>
>is Ok?

Yes. It actually compares 1 with the median of all.

Gordon

>Thanks,
>Mohammad Esad-Djou
>
>
> >
> > library(limma)
> > plotMA(data.exprs, array=3)
> >
> > if you want to compare the 3rd experiment, say, with the others?
> >
> > Gordon
>
>
>
>smyth@... schrieb am 30.03.05 14:05:26:
> >
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ivan.borozan | 1 Apr 2005 01:59
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question about multtest v.1.5.2

Hi there,

in multtest v.1.5.2 if i do

resT<-mt.maxT(mattest,cl,B=100)
ord<-order(resT$index)
rawp<-resT$rawp[ord]
maxT<-resT$adjp[ord]

i get for data that are not available (i.e NA's) 

rawp[1]
[1] NA
maxT[1]
[1] NA

...ect 

instead of 

rawp[1]
[1] 3.402823e+38
maxT[1]
[1] 3.402823e+38

...ect

as in the old version (1.0.2). Is this expected ?

R version 2.0.0, 2004-10-04, i686-pc-linux-gnu
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Salil | 1 Apr 2005 02:49

Memory issue

Hi Group,

Iam a beginner in learning R and Bioconductor.

I have a basic question. 
How can I increase the memory limit.

When I type the command:

abatch <- ReadAffy(filenames = myfilenames , phenoData = mypheno)

It throws me this error:

Error: cannot allocate vector of size 625759 Kb
In addition: Warning message: 
Reached total allocation of 511Mb

 
How can I overcome this?

Thanks

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Wolfgang Huber | 1 Apr 2005 10:45
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Re: Memory issue


Dear Salil,

how much memory does your machine have? How many files are there in 
"myfilenames" and what chiptypes are they? You might get started with 
using fewer arrays; on the long run, getting more memory seems like a 
good idea.

You can also try the justGCRMA (package gcrma) and justRMA functions: 
The man page says:
  This method should require much less RAM than the conventional
  method of first creating an 'AffyBatch' and then running 'gcrma'.

  Cheers
   Wolfgang

Salil wrote:
> Hi Group,
>  
> Iam a beginner in learning R and Bioconductor.
>  
> I have a basic question. 
> How can I increase the memory limit.
>  
> When I type the command:
>  
> abatch <- ReadAffy(filenames = myfilenames , phenoData = mypheno)
>  
> It throws me this error:
>
(Continue reading)

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Claire Wilson | 1 Apr 2005 11:03
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RE: Detection call for Hu6800

Hi Christian,

This error arises because simpleaffy doesn't know what the alpha1 and
alpha2 values are for the Hu6800 chips and you need to supply them with
the call to detection.p.val

pv17 <- detection.p.val(M17, alpha1=X,alpha2=Y) 

Hope this helps

Claire

> -----Original Message-----
> From: bioconductor-bounces@... 
> [mailto:bioconductor-bounces@...] On Behalf Of 
> Christian.Stratowa@...
> Sent: 30 March 2005 09:08
> To: bioconductor@...
> Subject: [BioC] Detection call for Hu6800
> 
> Dear BioC people
> 
> Could it be that neither detection.p.value (simpleaffy) nor 
> mas5calls (affy)
> work with Hu6800 chips?
> 
> I get the following errors:
> 
> > M17 <- ReadAffy(filenames=c("M17.cel"))
> > dpv17 <- detection.p.val(M17)
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Burkhard Heil | 1 Apr 2005 11:10
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Read PDB files

Hi,

Is there any function for R to read in PDB files?

Cheers,
Burkhard

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James W. MacDonald | 1 Apr 2005 15:38
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Re: Memory issue

Salil wrote:
> Hi Group,
>  
> Iam a beginner in learning R and Bioconductor.
>  
> I have a basic question. 
> How can I increase the memory limit.
>  
> When I type the command:
>  
> abatch <- ReadAffy(filenames = myfilenames , phenoData = mypheno)
>  
> It throws me this error:
>  
> Error: cannot allocate vector of size 625759 Kb
> In addition: Warning message: 
> Reached total allocation of 511Mb

Well, if you only have 512Mb RAM, you can overcome it by buying more. If 
you have more than that, you need to set your command line option 
--max-mem-size= to whatever amount of RAM you have. If you are on 
Windows, you need to set this in the Target field of your R shortcut.

Jim

>  
>  
> How can I overcome this?
>  
> Thanks
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Zhijin Wu | 1 Apr 2005 16:28
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RE: gcrma problem

Since you have a special chip, will you check what "xy2i" function you
get with
  tmp <- get("xy2i", paste("package:", cdfpackagename, sep = ""))

Do you have NAs in pmIndex or subIndex?

You are right that the line
    tmp.exprs[pmIndex[subIndex]] = apm 
is  to assign the value from apm to tmp.exprs[pmIndex[subIndex]]. 

Jean

On Thu, 31 Mar 2005, Wenqiong Chen wrote:

> Hi, Jim and Zhijin:
> I found the problem with the probe package, and it turned out to be very
> much trivial! It is the problem with the quotation, in 
> >getProbePackage(disdiv712aprobe), the name of the probe package should
> be quoted! :-(
> 
> O.K, now, following each step in compute.affinities, I finally came to
> the "real" problem in the line
> > tmp.exprs[pmIndex[subIndex]] = apm
> Error: NAs are not allowed in subscripted assignments
> 
> I have checked vector "apm" and there is no NA, and the lengths of apm
> and tmp.exprs[pmIndex[subIndex]] are the same. Based on the code right
> before this line, the tmp.exprs[pmIndex[subIndex]] has all the NAs. Does
> this line try to assign the value from apm to
> tmp.exprs[pmIndex[subIndex]]?
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Giulio Di Giovanni | 1 Apr 2005 18:06
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Strange signal Log-Ratios with MA.RG

Hi to all,

I have a problem that really I cannot solve.

Some signal log-ratios given to me converting a RGlist with MA.RG(RG) are 
different from the ones calculated directly, that's the point:

Looking some .gpr files, I build a RGList with

RG <- read.maimages(source="genepix", ext="gpr)

and I obtain for the first 3 genes and the first sample the following Red 
and Green Foreground and Background intensities

RG[1:3,1]
An object of class "RGList"
$R
     63MG
[1,]  407
[2,] 4304
[3,]  531

$G
     63MG
[1,]  291
[2,] 3571
[3,]  394

$Rb
     63MG
(Continue reading)

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Yanqin Yang | 1 Apr 2005 19:35
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how to keep R as the latest version in the simple way?

Hi,

I am using R 2.0.0 version. Do I need to update to R 2.0.1? How could I keep my R as the latest version? I
downloaded R 2.0.1 tar file. Do you have to remove the old version and reinstall the new version? In that
case, I need install all the packages I installed for the old R. 
Do you have a better idea to do this in the simple way?

Thanks a lot!

Yanqin

		
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