[BioC] some basic questions

[Kasper Daniel Hansen]

On Fri, Dec 2, 2011 at 12:35 AM, anand m t <anandrox05 at gmail.com> 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??

If your advisor is asking you to do this, you should discuss all of
the above with him not with people on this email list who have no
background.  Based on your interpretation of what your advisor asks
you to do, I would say it is certainly different from what a
"standard" analysis is.  When discussing this with your advisor you
might want to ask him whether he is aware that affymetrix arrays
typically have many probes grouped into probesets.  You might want to
discuss how you could go about "functionally group them".  Wrt. the
last question you might want to look at
  http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp
and read the references on that page.

Please don't ask us to interpret what your advisor is asking you to do.

Kasper


>
> 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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>> >
>>
>
>
>
> --
> ******************************************************************
> Anand M.T
> School of Biotechnology (Bio-Informatics),
> International Instituteof Information Technology (I2IT),
> P-14, Rajiv Gandhi Infotech park,
> Hinjewadi,
> Pune-411 057.
> INDIA.
>
> "The secret of success comprised in three words.. Work, Finish & Publish" -
> Michael Faraday
>
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