[BioC] Working with Agilent 4X44k array,two color experiment

[Sean Davis]

Hi, Srikanth.

If you have an RGList object, you will probably want to do some
normalization?  Also, you probably want to find
differentially-expressed genes?  Both of these steps are also detailed
in the limma User Guide.  Have you done these steps or do you have
another method for finding differentially-expressed genes?

Sean


On Wed, Jun 22, 2011 at 1:35 PM, Srikanth Manda Srinivas
<srikanth at ibioinformatics.org> wrote:
> Hi all,
>
> I have gone through limma package and now able to work with Agilent 4x44k
> two color experiment. I have 22 arrays with normal and tumor tissue. I want
> to draw heatmap for only a set of 10 genes (from all) up-regulated. Please
> let me know how does one go about choosing a specific set from all RGLists
> loaded. Thanks in advance
>
> Regards,
>
>
>
> On Tue, Jun 21, 2011 at 8:59 PM, Srikanth Manda Srinivas <
> srikanth at ibioinformatics.org> wrote:
>
>> Thanks for quick reply
>>
>>
>> On Tue, Jun 21, 2011 at 6:55 PM, Yong Li <yong.li at zbsa.uni-freiburg.de>wrote:
>>
>>> Hello Sean,
>>>
>>> the the Agi4x44Preprocess package is only for one color Agilent arrays. I
>>> also think the limma package is the right choice as it should do the job for
>>> two color Agilent arrays.
>>>
>>> Best regards,
>>> Yong
>>>
>>> Sean Davis wrote:
>>>
>>>> On Tue, Jun 21, 2011 at 6:28 AM, Srikanth Manda Srinivas
>>>> <srikanth at ibioinformatics.org> wrote:
>>>>
>>>>> Hi Everyone,
>>>>>
>>>>> I would like to know if we have specific package to work with Agilent
>>>>> 4X44k
>>>>> array just like Affy. Please guide me how one go for generating HeatMaps
>>>>> and
>>>>> other analysis on this data. I am a newbie in this area.
>>>>>
>>>>
>>>> Take a look at the Agi4x44Preprocess package.  If you are new to
>>>> microarray data analysis using bioconductor, take a look at the limma
>>>> package and its documentation, particularly the user guide.
>>>>
>>>> Sean
>>>>
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>>
>>
>>
>> --
>> Srikanth Manda Srinivas
>> Ph.D. Student
>> Institute of Bioinformatics
>> Discoverer, 7th Floor,
>> International Technology Park,
>> Bangalore, India
>> Mob:+917259692031
>>
>>
>
>
> --
> Srikanth Manda Srinivas
> Ph.D. Student
> Institute of Bioinformatics
> Discoverer, 7th Floor,
> International Technology Park,
> Bangalore, India
> Mob:+917259692031
>
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>
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