[BioC] some basic questions

[anand m t]

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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> >
>



-- 
******************************************************************
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" -
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