How to analysis the this kind of data set?
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Xiao Shi ▴ 90
@xiao-shi-1184
Last seen 10.2 years ago
hi,everybody I have a *time course* data set about a CML cell line treated by two drugs and their combination.The experiment was performed on cDNA microarray platform.The green channel of all the arrays are common,the untreated cell.Here follows the experiment design: a_0hr,a_3hr,a_8hr,a_12hr,a_24hr,a_48hr,a_72hr, b_3hr,b_8hr,b_12hr,b_24hr,b_48hr,b_72hr, ab_3hr,ab_8hr,ab_12hr,ab_24hr,ab_48hr,ab_72hr. A total of 19 *cDNA microarrays*.a_0hr means* *drug *a *treament *0 hours vs. control. *And a_3hrs means drug a treatment 3 hours vs. control.So for drug *b *and their combination *ab*(drug a and drug b added together).My goal is to identify the three sets of genes,the genes differentially expressed by drug a,the genes by drug b ,and their combination. i am thinking about *ANOVA* ,but i am not sure whether it is correct. Any comments,suggestions?Any R/bioconductor packages can be used?Thanks in advance [[alternative HTML version deleted]]
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@rhonda-decook-1033
Last seen 10.2 years ago
Hi Xiao, It seems in a design such as this with Treatment and Time, there are a lot of ways to define 'differential expression'. You say you're looking for differentially expressed genes with respect to treatment(a,b,ab). So, does this mean you're not interested in any time effects(or any Treatment- by-Time interactions)? Maybe you're looking for genes where the three expression profiles over time are parallel for the different treatments, but one of these profiles is 'far away' from the other two? Rhonda > hi,everybody > I have a *time course* data set about a CML cell line treated by two drugs > and their combination.The experiment was performed on cDNA microarray > platform.The green channel of all the arrays are common,the untreated > cell.Here follows the experiment design: > > a_0hr,a_3hr,a_8hr,a_12hr,a_24hr,a_48hr,a_72hr, > b_3hr,b_8hr,b_12hr,b_24hr,b_48hr,b_72hr, > ab_3hr,ab_8hr,ab_12hr,ab_24hr,ab_48hr,ab_72hr. > > A total of 19 *cDNA microarrays*.a_0hr means* *drug *a *treament *0 hours > vs. control. *And a_3hrs means drug a treatment 3 hours vs. control.So for > drug *b *and their combination *ab*(drug a and drug b added together).My > goal is to identify the three sets of genes,the genes differentially > expressed by drug a,the genes by drug b ,and their combination. > i am thinking about *ANOVA* ,but i am not sure whether it is correct. > Any comments,suggestions?Any R/bioconductor packages can be used?Thanks in > advance > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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Hi Xiao; I think maybe you want to identify differentially expressed genes under treatment (a,b,ab) compared to untreated group, across all time points. Say X=log(R/G) (a vector of 6 as the log ratio of red and green intensities across 6 common time.) H0: X=0 vs Ha: X!=0 If you don't have replications, ANOVA is not possible if you treat time as a factor. There are some publications on this topic, just search pubmed with key words "time course" Fangxin > Hi Xiao, > > It seems in a design such as this with Treatment and Time, there are a lot > of > ways to define 'differential expression'. You say you're looking for > differentially expressed genes with respect to treatment(a,b,ab). So, > does > this mean you're not interested in any time effects(or any > Treatment-by-Time > interactions)? Maybe you're looking for genes where the three expression > profiles over time are parallel for the different treatments, but one of > these > profiles is 'far away' from the other two? > > Rhonda > > > >> hi,everybody >> I have a *time course* data set about a CML cell line treated by two >> drugs >> and their combination.The experiment was performed on cDNA microarray >> platform.The green channel of all the arrays are common,the untreated >> cell.Here follows the experiment design: >> >> a_0hr,a_3hr,a_8hr,a_12hr,a_24hr,a_48hr,a_72hr, >> b_3hr,b_8hr,b_12hr,b_24hr,b_48hr,b_72hr, >> ab_3hr,ab_8hr,ab_12hr,ab_24hr,ab_48hr,ab_72hr. >> >> A total of 19 *cDNA microarrays*.a_0hr means* *drug *a *treament *0 >> hours >> vs. control. *And a_3hrs means drug a treatment 3 hours vs. control.So >> for >> drug *b *and their combination *ab*(drug a and drug b added together).My >> goal is to identify the three sets of genes,the genes differentially >> expressed by drug a,the genes by drug b ,and their combination. >> i am thinking about *ANOVA* ,but i am not sure whether it is correct. >> Any comments,suggestions?Any R/bioconductor packages can be used?Thanks >> in >> advance >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- Fangxin Hong, Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong@salk.edu
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