marginal3617 | 1 Sep 01:19 2007

Fwd: Re: einem schnellen One- Night- Stand- Ficken ( Grund)

N A M E : Leona, A L T E R : 33, B E R U F : Hausfrau

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der mich wieder mal so richtig durchbumst! Wenn du also mein Lover sein willst, egal ob fur eine Nacht oder
fur Langzeitbeziehungen, ich bin fur beides zu haben! 

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dort meine Heimadresse und meine Handynummer hinterlassen, melde dich bei mir und besuche mich, oder ich
komme zu dir.

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Deine scharfe LEONA -:) 

Wenn Du diesen Newsletter nicht mehr erhalten mochtest, klicke einfach auf diesen Link:
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J.delasHeras | 1 Sep 02:46 2007

Re: Analysis of many Flagged spots

Quoting Davide Valentini <Davide.Valentini@...>:

> Hi to all,
> I've to deal with a dataset that has a huge amount of flagged as "bad"
> spots. My data are from peptide microarrays and the proportion of flags
> is around the 90% in each slide. Luckily I have a good set of samples
> (35 cases and 35 controls), but I'm not an expert with this kind of
> problem. Should I treat the flagged data as missing values and so try to
> impute new values instead the flagged "bad" spots ? I know the KNN
> imputation or the SVD imputation.
> What is normally done with the spots flagged as "bad" (-100, following
> GenePix criteria + additional criteria) in cDNA experiments ?
> Sorry if the question looks banal, but as I said I'm not an expert on
> this field. Any help is useful, also links regarding flagged data
> analysis...
> Thanks in advance,
> Davide

Hi Davide,

when looking at the actual images, are the high number of "bad" spots  
indicating artifacts on the slides (dirt, scratches, high and uneven  
background...) or just a reflection of your probes lighting up just a  
small proportion of the spots?
(Continue reading)

Gordon Smyth | 1 Sep 03:01 2007

topTable changes

Hi Sue,

Your question doesn't make a lot of sense, because there have been no 
changes to the p-value columns output by topTable. The adj.P.Val 
column still exists as it always has, and there never has been a 
columun called "P".

As pointed out by Jose, the problem is more likely to be that you are 
using the column tab$M which is now called tab$logFC.

limma comes with lots of documentation. Why not just type


to see exactly what the columns are and what they mean?



would tell you the column names.

Best wishes

>Date: Thu, 30 Aug 2007 17:30:24 +0100 (BST)
>From: Sue Jones <s.jones@...>
>Subject: [BioC] topTable changes
>To: bioconductor@...
(Continue reading)

William Shannon | 1 Sep 21:55 2007

aCGh data analysis and new journal


  I have been working with comparative genomic hybridization data for 4 years related to the genomics of AML. 
I submitted a manuscript (on Tuesday) that outlines an approach based on statistical process control for
analyzing this data.  In this framework we are able to analyze 2.1 million probe nimblegen arrays rapidly.

  I cannot circulate the manuscript now (it's under review) but would encourage anyone working with CGH data
to look into process control methods.  This is a vast set of tools from industrial statistics (think
Deming) that fit the CGH data framework ideally -- 2 copies of a gene is in cotrol and
amplifications/deletions are out of control.

  I submittred my manuscript as an invited paper to a new excellent journal that I suggest you consider for
your papers:  It is focused on
applications and I think will be an excellent venue for the type of work and problems discussed on this list.

  Bill Shannon, PhD
BioRankings, LLC
Founder and President

  "Helping you gain understanding of statistical data to protect your investment."

  Associate Professor of Biostatistics in Medicine
Washington University School of Medicine

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Tobias Verbeke | 2 Sep 08:18 2007

buglet (?) snprma (oligo)

Dear list,

I discovered an oddity in snprma (oligo,
svn revision 26822). It appears that ranks
are used to extract elements from vectors in

     for (i in 1:ncol(tmpExprs))
       tmpExprs[, i] <- reference[rank(tmpExprs[, i])]

This might break iff there are two values that
are exactly equal as can be seen from

   bar <- 2 * c(2, 4, 4, 5, 1)
   foo <- 1:5

A solution would be to specify an alternative
ties.method such as

   rank(bar, ties.method = "first")

Any thoughts?




Tobias Verbeke - Consultant
(Continue reading)

Markus Schmidberger | 3 Sep 08:26 2007

ReadAffy Error


the ReadAffy function is no longer working on my windows machine. This 
code was working last week (and still on my linux system), then I 
installed Rtools (, now I get 
an error. (I think I changed nothing else)

path <- "Z:/Microarray/hgu133a-spikein/rawdata"
celFile <- list.celfiles(path=path,full.names=TRUE);
affyBatch <- ReadAffy(filenames=celFile[1:3]);

Fehler in int.unzip(file.path(path, zipname), topic, tmpd) :
        'destination' existiert nicht

The vector celFile is made up celFiles, no zip files. The data used, are 
CEL files from affycomp

23: zip.file.extract(file, "")
22: data(mapCdfName, envir = environment())
21: cleancdfname(cdfname, addcdf = FALSE)
20: .nextMethod(.Object, ...)
19: eval(expr, envir, enclos)
18: eval(call, callEnv)
17: callNextMethod(.Object, ...)
16: .local(.Object, ...)
15: .nextMethod(.Object, assayData = assayData, phenoData = phenoData,
        featureData = featureData, experimentData = experimentData,
        annotation = annotation)
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Sylvia Merk | 3 Sep 09:55 2007

Re: ReadAffy Error

Hi Markus,

I think the problem lies in the way you define the path. 
When I remember some earlier experiences with R on windows you should
use something like 

path <- "z:\\\\Microarray\\hgu133-spikein\\rawdata"

What happens when you change to the cel-file-directory and use



Dr. Sylvia Merk
Department of Medical Informatics & Biomathematics
University of Muenster
Domagkstr. 9
D-48149 Muenster
Tel.: ++49-251-83-52498
Fax: ++49-251-83-55277

Am Montag, den 03.09.2007, 08:26 +0200 schrieb Markus Schmidberger:
> Hello,
> the ReadAffy function is no longer working on my windows machine. This 
> code was working last week (and still on my linux system), then I 
(Continue reading)

Markus Schmidberger | 3 Sep 10:07 2007

Re: ReadAffy Error


no, then there is the error:
celFile <- 
Warning message:
list.files: 'Z:\\Microarray\hgu133-spikein\rawdata' ist kein lesbares 
Verzeichnis in: list.files(...)

I think it is not a path problem. list.celfiles generates the right 
vector with Cel files.


Sylvia Merk schrieb:
> Hi Markus,
> I think the problem lies in the way you define the path. 
> When I remember some earlier experiences with R on windows you should
> use something like 
> path <- "z:\\\\Microarray\\hgu133-spikein\\rawdata"
> What happens when you change to the cel-file-directory and use
> ReadAffy()?
> Best, 
> Sylvia
(Continue reading)

Pedro López-Romero | 3 Sep 10:36 2007

Receive your own posts to the list

Hi all, 

Since a couple of months, I don’t receive a copy of the mails that I post to
the list, even when I click on “replay to all”  to answer a message by other
user. I have checked the “ Receive your own posts to the list” option and it
is activated, so I do not know where the problem is.- Does anyone know how
to solve this little problem?

Thank you 


Checked by AVG Free Edition. 


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STKH (Steen Krogsgaard | 3 Sep 11:42 2007

Re: Receive your own posts to the list

Hi Pedro,

maybe your own posts gets chopped by your spam filter. When I post, my spam filter tags the message as
putative spoofing as the mail seems to origin from me but is send from another sender. Maybe your spam
filter does the same thing but removes the message instead of tagging it.


Best Regards
Steen Krogsgaard
Novozymes A/S (reg. no.: 10007127)
Krogshoejvej 36
Bagsvaerd, 2880, Denmark
Phone: +45 44427166
Mobile: +4530797166
E-mail: stkh@...

This e-mail (including any attachments) is for the intended addressee(s) only and may contain
confidential and/or proprietary information protected by law. You are hereby notified that any
unauthorized reading, disclosure, copying or distribution of this e-mail or use of information herein
is strictly prohibited. If you are not an intended recipient you should delete this e-mail immediately.
Thank you.

-----Original Message-----
From: bioconductor-bounces@...
[mailto:bioconductor-bounces <at>] On Behalf Of Pedro López-Romero
Sent: 3. september 2007 10:36
To: bioconductor@...
Subject: [BioC] Receive your own posts to the list
(Continue reading)