Hi,

This is very tedious, but I have a lot of trouble reading the adf file of
an Agilent chip I attached here. I try to read it with the script.

>read.table("9712.adf.txt", skip=11, sep = "\t", header = FALSE, as.is =
TRUE)[,c(2,5)]

Then R shows..
>Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
 :
  line 512 did not have 17 elements

What should I do?

Best,
Kaj

On Sat, Feb 16, 2013 at 11:30 PM, Kaj Chokeshaiusaha <
kajkajkajkajkaj@gmail.com> wrote:

> Dear All,
>
> Sorry for my previous confusing mail. I've found the corresponding .adf of
> 'Agilent-015354 Bovine Oligo Microarray (4x44K)' in eArray.
>
> Best Regards,
> Kaj
>
>
> On Sat, Feb 16, 2013 at 10:20 PM, Kaj Chokeshaiusaha <
> kajkajkajkajkaj@gmail.com> wrote:
>
>> 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@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> 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>
>>>>
>>>> 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.
>>>>>>
>>>>>> ______________________________**_________________
>>>>>> Bioconductor mailing list
>>>>>> Bioconductor@r-project.org
>>>>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.ch/mailman/listinfo/bioconductor>
>>>>>> Search the archives: http://news.gmane.org/gmane.**
>>>>>> science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>>>>>
>>>>>
>>>>> --
>>>>> 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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