Question: normalization and clustering etc...
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16.5 years ago by
Phguardiol@aol.com720 wrote:
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 [[alternate HTML version deleted]]
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