[BioC] Bioconductor Digest, Vol 31, Issue 7
Shruti Subramaniam
ssubra3 at emory.edu
Thu Sep 8 14:07:55 CEST 2005
Sorry about the email. My mailbox got infected with a virus and is sending
out weird emails from my sent email to all.
Thanks
-----Original Message-----
From: Shruti Subramaniam [mailto:ssubra3 at emory.edu]
Sent: Thursday, September 08, 2005 8:00 AM
To: 'bioconductor at stat.math.ethz.ch'
Subject: RE: Bioconductor Digest, Vol 31, Issue 7
Are meri ganji,
Photo attach hi kaha kiya tune mail ke sat.
Send me the photos duffy to react.
Love
Shruti
-----Original Message-----
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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 at 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 at 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 at 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 at 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 at 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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