[BioC] some basic questions

[Richard Friedman]

Dear Anand,

 	I am not sure what you advisor means by "functionally group".

Best wishes,
Rich



On Fri, 2 Dec 2011, anand m t wrote:

> Dear Dr. Friedman,
>
> Thank you for the notes again. It was really helpful and my many questions
> got cleared after going through it.
> But what my adviser asking me to do is, i've normalized data (54 k probes),
> he's asking me to functionally group them all.
> After that, he wants me to perform significance test within each group to
> find out deferentially expressed genes.
> My question is how's that different from conventional way of finding DE
> genes and functionally grouping them ?? Is it valid??
>
> Dear Sean,
>
> I've data from HGU133 plus 2 array. I followed through the links but still
> i'm confused. I've attached a file for reference [this'a screen shot of a
> published data].
> In the attachment, the transcript audacin 3 gamma, is represented by 4
> different probe ID's and all are showing different intensity values.
> Now i want filter those probe ID's with significant deviation, from further
> analysis. How do i get this data of different probe's representing the same
> trascript ??
>
> Again sorry if my questions are lame, i'm new to microarray analysis and
> i'm getting confused and lost.
>
>
> On Wed, Nov 30, 2011 at 8:16 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> On Wed, Nov 30, 2011 at 2:04 AM, anand mt [guest]
>> <guest at bioconductor.org> wrote:
>>>
>>> Hi all..
>>>
>>> i have following questions.
>>>
>>> 1) How many probesets represent a gene on microarray chip ?
>>>
>>
>> That depends on the array platform.  For a given platform, you can use
>> the annotation packages to answer this question.  To get started, take
>> a look at:
>>
>> http://bioconductor.org/help/workflows/annotation-data/
>>
>>> 2) How do i access raw intesity value of probes (before normalization) ?
>>
>> This will depend on the array platform and the software package you
>> are using to do your analysis.  Some specifics are probably needed.
>> To get started, be sure to take a look at:
>>
>> http://bioconductor.org/help/workflows/oligo-arrays/
>>
>>> 3) Do i need to read cdf file to do that ??
>>
>> Generally not.  Depending on the software package that applies, the
>> data from the CDF file are usually repackaged for use in bioconductor.
>>  Again, some specifics of your data and experiment are important.
>>
>>> 4) After pre-processing the data and normalization, we generally go for
>> significance tests and gene grouping. My question is, if i group the genes
>> before performing  significance test (say now i have 3 groups based on
>> apoptosis,cell cycle, DNA replication) and then perform significance test
>> within each group, will the results be same as that of conventional way ??
>> Is it a valid method to do so??
>>>
>>
>> You might take a look at this question and response on biostar:
>>
>>
>> http://biostar.stackexchange.com/questions/14796/gene-expression-analysis-microarrays-geneset
>>
>> Hope that helps.
>>
>> Sean
>>
>>
>>> Sorry if my questions are silly.
>>>
>>>  -- output of sessionInfo():
>>>
>>> --NONE--
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>>
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>>
>
>
>
>

-- 
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Biomedical Informatics Shared Resource
Lecturer
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
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friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

"The last 250 pages of the last Harry Potter
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place in one day and nothing happened in that day."
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