[BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms
James W. MacDonald
jmacdon at uw.edu
Mon Feb 18 16:19:59 CET 2013
Hi Kaj,
First some admonishment. You appear not to be trying very hard to figure
out how to do this on your own. I gave you some pretty clear
instructions that you need a file that has two columns, one with the
probe IDs and one with some other annotation ID. I then pointed you to
the vignette that shows how to create the package.
So you then went out and found a file that looks promising. It is called
the 015354 somethingsomething genelist, and that corresponds to your
array. So good for you.
But then you came back to us to see if it is OK. This is a problem, as
you will never get far with OpenSource software if you aren't willing to
figure things out on your own (especially if you have already been told
explicitly what you need to do).
Rather than telling you what to do next, let's try the Socratic approach.
1.) What data are represented in this file? Do they perhaps fulfill one
of the requirements for AnnotationForge? If you think not, why do you
think that? If you think they do, why are you asking us?
2.) If this file does contain data sufficient for building an annotation
package, what do you need to do in order to proceed from here? Have you
read the vignette? Do you not understand something?
Don't be afraid to try things. You are very unlikely to break anything,
and failing is the best way to learn. If/when you fail, try to figure
out on your own why the failure occurred. Google is your friend.
If you want to learn how to analyze data using Bioconductor you will
need to become self-reliant. People are amazingly willing to help people
who are truly struggling, and have tried their best to progress. They
are much less willing to help those who seem not to help themselves.
If you try and fail, don't be afraid to come back with questions. But be
prepared to show what you have tried, and supply the error message. Also
supply the output of sessionInfo().
Best,
Jim
On 2/16/2013 10:20 AM, Kaj Chokeshaiusaha wrote:
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> Dear All,
>
> I hope this won't be too tedious for you, please be patient with me.
>
> I have found the bovine gene list from Agilent
> (http://www.chem.agilent.com/cag/bsp/gene_lists.asp).
>
> Is this what I need for making db package?
>
> Best Regards,
> Kaj
>
> On Fri, Feb 15, 2013 at 7:54 PM, Kaj Chokeshaiusaha
> <kajkajkajkajkaj at gmail.com <mailto:kajkajkajkajkaj at gmail.com>> wrote:
>
> Dear All,
>
> I have loaded AnnotationForge. I will try my best to understand
> it. I will certainly come up with more questions. Thank you very
> much for your helps.
>
> Best Regards,
> Kaj
>
>
> On Fri, Feb 15, 2013 at 4:54 PM, Andreas Heider
> <aheider at trm.uni-leipzig.de <mailto:aheider at trm.uni-leipzig.de>>
> wrote:
>
> Dear Kaj,
> Jim was mostly correct. You will have to setup a annotation
> package for your bovine chip, but don't worry, you can use
> Affymetrix' annotation files to get it done using
> AnnotationForge. For your Rhesus chip you could try to use the
> org.Mmu.eg.db or rhesus.db0 packages, but will need to convert
> your probesets into some gene/transcript identifier first
> using Affymetrix' annotations. Your mouse data can be used
> directly using one of the mogene10* annotation packages, as
> Jim already pointed out.
>
> Your approach involves some work, but is definitely possible.
>
> Cheers,
> Andreas
>
>
> 2013/2/14 James W. MacDonald <jmacdon at uw.edu
> <mailto:jmacdon at uw.edu>>
>
> Hi Kaj,
>
>
> On 2/14/2013 11:48 AM, Kaj Chokeshaiusaha [guest] wrote:
>
> Dear whom it may concern,
>
> I'm working with the platforms as following:
> 1. Agilent-015354 Bovine Oligo Microarray (4x44K)
>
>
> I don't think there is a .db package for this one. You
> could go to earray
> (https://earray.chem.agilent.com/earray/) and find the
> correct GeneList, and then use AnnotationForge to create
> one. It could be fun, and help you break out of that 'pure
> biologist' rut you appear to be in ;-D
>
>
> 2. Affymetrix GeneChip Rhesus Macaque Genome Array
> [Rhesus]
>
>
> biocLite("rhesus.db")
>
>
> 3. Affymetrix GeneChip Mouse Gene 1.0 ST Array
>
>
> biocLite("mogene10sttranscriptcluster.db")
>
> assuming that you have summarized at the transcript level
> (and IMO you should).
>
> Best,
>
> Jim
>
>
>
> Since I'm quite pure biologist, I do have no idea how
> to find appropriate annotations (.db) for these
> platforms. I need to use them for virtaulArray.
>
> Would you please help me?
>
> Best Regards,
> Kaj
>
> -- output of sessionInfo():
>
> sessioninfo()
>
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> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
>
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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