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Shruti Subramaniam
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-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of
bioconductor-request at stat.math.ethz.ch
Sent: Thursday, September 08, 2005 6:00 AM
To: bioconductor at stat.math.ethz.ch
Subject: Bioconductor Digest, Vol 31, Issue 7
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Today's Topics:
1. Re: Writing own package description. (Judith Offman)
2. Re: Writing own package description. (James W. MacDonald)
3. Re: Writing own package description. (James W. MacDonald)
4. Re: Writing own package description. (Sean Davis)
5. SpotTypes doesn't match (Gordon Smyth)
----------------------------------------------------------------------
Message: 1
Date: Wed, 7 Sep 2005 11:12:24 +0100
From: Judith Offman <jo41@sussex.ac.uk>
Subject: Re: [BioC] Writing own package description.
To: TEXTORIS Julien <julien.textoris at="" gmail.com="">
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <f4c7fa11-5b12-46f7-879a-c9c308f74bb2 at="" sussex.ac.uk="">
Content-Type: text/plain
Hi,
I have also only just started using bioc and I would be very
interested in doing some of the tutorials you mentioned, especially
the ones for affy data, as I am using these chips.
Where can I find these tutorials?
Thanks for your help,
Judith
On 6 Sep 2005, at 21:27, TEXTORIS Julien wrote:
> Hi,
>
> i've learn through the many tutorials and courses available on the
net
> (thanks to everybody for that, it's wonderfull), and i really like
> working with bioc.
>
> I work in a lab where we use a cDNA, home made chip. I was
> wondering how
> i could write a package for R to describe this particular chip, and
> use
> all the possibility of bioconductor with it, because all that i
> learned
> with tutorials was with affy chips.
>
> I've read some documents but i'm still a bit confused about that.
> The exprset structure is for data, isn't it ? So in it, i'll put
> results
> from my experiments, and also phenoData. But i also need to describe
> which probe correspond to which gene ? no ?
>
>
> How could i start ?
>
> thanks for your answers.
>
> Julien Textoris
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
Dr Judith Offman
Genome Damage & Stability Centre
Science Park Road
University of Sussex
Falmer
Brighton BN1 9RQ
Telephone: 01273-678976
Fax: 01273-678121
E-mail: jo41 at sussex.ac.uk
[[alternative HTML version deleted]]
------------------------------
Message: 2
Date: Wed, 07 Sep 2005 08:42:58 -0400
From: "James W. MacDonald" <jmacdon@med.umich.edu>
Subject: Re: [BioC] Writing own package description.
To: bioconductor at stat.math.ethz.ch
Message-ID: <431EE052.80905 at med.umich.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Judith Offman wrote:
> Hi,
>
> I have also only just started using bioc and I would be very
> interested in doing some of the tutorials you mentioned, especially
> the ones for affy data, as I am using these chips.
> Where can I find these tutorials?
Most are here:
http://www.bioconductor.org/workshops/
You might also want to start with the vignettes, which can be
accesssed
by typing openVignette() after loading e.g., the affy package. You can
also step through the code in a vignette by loading the tkWidgets
package and then typing vExplorer() at an R prompt.
Alternatively, you can browse the vignettes here:
http://www.bioconductor.org/docs/vignettes.html
Best,
Jim
>
> Thanks for your help,
> Judith
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
------------------------------
Message: 3
Date: Wed, 07 Sep 2005 08:54:15 -0400
From: "James W. MacDonald" <jmacdon@med.umich.edu>
Subject: Re: [BioC] Writing own package description.
To: TEXTORIS Julien <julien.textoris at="" gmail.com="">
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <431EE2F7.9060304 at med.umich.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
TEXTORIS Julien wrote:
> Hi,
>
> i've learn through the many tutorials and courses available on the
net
> (thanks to everybody for that, it's wonderfull), and i really like
> working with bioc.
>
> I work in a lab where we use a cDNA, home made chip. I was wondering
how
> i could write a package for R to describe this particular chip, and
use
> all the possibility of bioconductor with it, because all that i
learned
> with tutorials was with affy chips.
I am not sure you need to write a package for any of this. There are
already packages in BioC that are designed to normalize (marray,
limma)
and make comparisons (limma, multtest, factDesign) using cDNA arrays.
I suppose there may be some functionality you might like that is not
implemented in these packages, but I would recommend starting with the
existing packages. IIRC, all of these packages have vignettes, so that
would probably be the best place to start.
Best,
Jim
>
> I've read some documents but i'm still a bit confused about that.
> The exprset structure is for data, isn't it ? So in it, i'll put
results
> from my experiments, and also phenoData. But i also need to describe
> which probe correspond to which gene ? no ?
>
>
> How could i start ?
>
> thanks for your answers.
>
> Julien Textoris
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
------------------------------
Message: 4
Date: Wed, 07 Sep 2005 10:09:04 -0400
From: Sean Davis <sdavis2@mail.nih.gov>
Subject: Re: [BioC] Writing own package description.
To: "James W. MacDonald" <jmacdon at="" med.umich.edu="">, TEXTORIS
Julien
<julien.textoris at="" gmail.com="">
Cc: Bioconductor <bioconductor at="" stat.math.ethz.ch="">
Message-ID: <bf446cc0.dd29%sdavis2 at="" mail.nih.gov="">
Content-Type: text/plain; charset="US-ASCII"
On 9/7/05 8:54 AM, "James W. MacDonald" <jmacdon at="" med.umich.edu="">
wrote:
> TEXTORIS Julien wrote:
>> Hi,
>>
>> i've learn through the many tutorials and courses available on the
net
>> (thanks to everybody for that, it's wonderfull), and i really like
>> working with bioc.
>>
>> I work in a lab where we use a cDNA, home made chip. I was
wondering how
>> i could write a package for R to describe this particular chip, and
use
>> all the possibility of bioconductor with it, because all that i
learned
>> with tutorials was with affy chips.
>
> I am not sure you need to write a package for any of this. There are
> already packages in BioC that are designed to normalize (marray,
limma)
> and make comparisons (limma, multtest, factDesign) using cDNA
arrays.
>
> I suppose there may be some functionality you might like that is not
> implemented in these packages, but I would recommend starting with
the
> existing packages. IIRC, all of these packages have vignettes, so
that
> would probably be the best place to start.
We also use custom arrays. It suffices to write a little function to
load
the data into the data structures provided by one of the "major
players"
like limma or marray. Then, all of the tools associated with those
packages
are available.
The other package to look into, if you are really bioconductor-
centric, is
AnnBuilder which allows you to build an annotation package for your
array.
Sean
------------------------------
Message: 5
Date: Thu, 08 Sep 2005 10:30:21 +1000
From: Gordon Smyth <smyth@wehi.edu.au>
Subject: [BioC] SpotTypes doesn't match
To: kevin Lin <khlin at="" odin.mdacc.tmc.edu="">
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <6.2.1.2.1.20050908102731.0211ca88 at
imaphost.wehi.edu.au>
Content-Type: text/plain; charset="us-ascii"; format=flowed
I suspect you will find that there is no column called "controltype"
in
your GPR files. Perhaps check the capitalisation.
Gordon
>Date: Tue, 6 Sep 2005 14:47:22 -0500
>From: kevin Lin <khlin at="" odin.mdacc.tmc.edu="">
>Subject: [BioC] SpotTypes doesn't match
>To: <bioconductor at="" stat.math.ethz.ch="">
>Message-ID: <a06002001bf439982ab56@[143.111.133.119]>
>Content-Type: text/plain; charset="us-ascii" ; format="flowed"
>
>Hi BioC,
>
>I am using Limma, the problem occurs in my 2nd object
RGgpr$genes$Status.
>
> > SpotTypes
> SpotType controltype Name color
>1 cDNA * * black
>2 genes FALSE * grey
>3 positive positive * blue
>4 ignore ignore * orange
>5 notprobe notprobe 0 yellow
>
> > RGgpr$genes$Status <- controlStatus(SpotTypes, RGgpr$genes)
>Matching patterns for: Name
>Found 11592 cDNA
>Found 11592 genes
>Found 11592 positive
>Found 11592 ignore
>Found 664 notprobe
>Setting attributes: values controltype color
>
>I cut and pasted two columns (Name and controltype) of *.gpr files to
>confirm the different numbers of controltypes.
> >table(read.table("twoColumns.txt",sep='\t',header=F))
>FALSE ignore notprobe positive
> 8564 2112 664 252
>
>Q1, Why did they give me the same # 11592 ? Is it because I used wild
>card "*" ? Can this be fixed?
>Q2, If so, what can i do with the SpotType.txt to fixed the problem ?
>
>Thanks for any help
>
>Kevin
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