Dear all,

Thanks for your admonishment. I will try better.

The adf file here is the details of the bovine Agilent platform I'm trying
to create annotation. It's just because my weak R, I can't read it in table.

Now I can read it by adding 'fill=TRUE' in the command.

After reading your advice, In fact, I do have two things disturbing me a
lot.

1. To create the two column file, I decide to have 'ProbeID' and 'Genebank
ID'. I choose them because they show corresponding data in every line with
no missing data. I don't know this is the correct way to choose them or not.

2. I do have trouble with dbschemas for 'makeDBPackage' function in R.
There are two dbschemas; BOVINE_DB and BOVINECHIP_DB. I can't find the
details of these files. In fact, I don't even understand dbschemas. What
should I choose here and how to check it? I'm very scared to acquire the
false Annnotation package due to this step.

I'm tremedously sorry for the previous mail. I must admit that I get
nervous and confused. I'm the only one here to use R and interested in the
field, so I get anxious quite frequently. I deeply apologize you all.
Please help me.

Best Regards,
Kaj



On Mon, Feb 18, 2013 at 10:19 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> 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<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@gmail.com <mailto:kajkajkajkajkaj@gmail.**com<kajkajkajkajkaj@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@trm.uni-leipzig.de <mailto:aheider@trm.uni-**leipzig.de<aheider@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@uw.edu
>>         <mailto:jmacdon@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/<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()
>>
>>                 --
>>                 Sent via the guest posting facility at
>>                 bioconductor.org <http://bioconductor.org>.
>>
>>
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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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