[BioC] normalization and clustering etc...
Phguardiol at aol.com
Phguardiol at aol.com
Sat Apr 5 05:31:07 MEST 2003
Hi all,
I have recently discover Cyber-T and I was wondering if this Bayesian
approach for comparison was available in Bioconductor since I dont always
have a fast internet connection and I m not working on Unix / Linux yet ?
What seems to be a similar approach is apparently available in the new S+
module Array analyzer is it also in R/Bioconductor ?
In the same way, is there any kind of Bayesian clustering method available in
Bioconductor like the one available in Array Miner ?
In addition, I have two questions that I d like to have some help about from
your group:
I ve affy 133A+B chips made from RNA coming from 4 cell lines. Two of these
cell lines are B cells (one has a deficient gene and the other has the
corrected gene inserted instead of the deficient one, both are coming from
the same parental cell line) and 2 others are fibroblastic cell lines in
which the same gene is inactivated or not. Therefore I have 2 cell lines
deficient for a gene C (one fibroblast one B cell) and their corrected
homologs. In addition, all these cells have been exposed to the same
chemotherapeutic agent at the same dose same duration so that I have data
from untreated and treated cells. I am planning to compare corrected versus
uncorrected untreated B cells, then the same for fibroblasts, then all this
again for treated cells. The aim is to isolate genes that are differentially
expressed in nornal conditions between the deficient and corrected B cells
then the same for the fibroblasts and then finally to see which one are in
both cases differentially expressed. Finally I d like to know what are the
modifications of these results when I stress the cells with chermo. So here
are my qurestions:
- For normalization: should I normalize the whole set of chips then do all my
comparisons or should I normalize only the chips I am planning to compare at
each time and repeat this process for each comparison ? I m planning to use
the RMA module.
- For clustering: I have identified at least one gene W of great interest in
my model and I was planning to do clustering analysis to see what are the
genes with a similar pattern of expression. Using all my differents
conditions with my 4 cell lines I found one very interesting gene Z in the
cluster of the first gene W. I was wondering if it would be a good idea to
add some extra chips made from completely different cells, ie, CD34+
hematopoietic stem cells, mature Cd22+ B cells, acute leukemia cell lines in
my case, as a validation process ? For instance, if the gene Z is not anymore
close to gene W with these extra chips... what could be the conclusion...?
Thanks for your help
Philippe
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