Question: interaction term contrast in Weaver mutant example of LIMMA manual
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gravatar for Erika Melissari
10.2 years ago by
Erika Melissari240 wrote:
Dear bioconductor list, I am studing the Weaver experiment example of LIMMA manual and I am in a maze about the biological meaning of interaction term present among the contrasts. I did not manage to understend what kind of differentially expressed gene this contrast takes-out. The interaction contrast is: (P21mt-P11mt)-(P21wt-P11wt) The first bracket takes-out the differentially expressed genes between the mutant subjects at two different time points(21 and 11 minutes) and the second bracket those between the wild-type subject at the same different time points. ..but what differentially expressed genes takes-out the global interaction contrast? In order to evaluate an interaction do I need absolutely the four arrays in direct comparison done in this example? Thank you very much for any explaination Erika
limma weaver • 553 views
ADD COMMENTlink modified 10.2 years ago by James W. MacDonald51k • written 10.2 years ago by Erika Melissari240
Answer: interaction term contrast in Weaver mutant example of LIMMA manual
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gravatar for James W. MacDonald
10.2 years ago by
United States
James W. MacDonald51k wrote:
Hi Erika, Erika Melissari wrote: > Dear bioconductor list, > > I am studing the Weaver experiment example of LIMMA manual and I am in a > maze about the biological meaning of interaction term present among the > contrasts. > I did not manage to understend what kind of differentially expressed gene > this contrast takes-out. In this experiment we can look at genes that change between the two time points in the mutant samples, or that change between the two time points in the wild type samples. In addition, we might be interested in those genes that react differently in the two sample types. In other words, a particular gene might increase expression in the wild type samples, but actually decrease expression in the mutant samples. This third comparison is known as an interaction. > The interaction contrast is: > > (P21mt-P11mt)-(P21wt-P11wt) Correct. So using our example from above, the first term will be negative (since the expression level went down in mutant samples). The second term will be positive, since the expression went up over time in the wild type samples, but since we subtract, we end up with a (possibly) large negative number. The same will be true of any scenario you can envision where the mutant and wild type samples react differently to the incubation time. Another example would be the situation where the mutant samples were up-regulated at 21 hours, but the wild type samples were unaffected. In this case you can see that we might have a large value for this contrast. However, if both wild type and mutant samples were up-regulated approximately the same amount, the resulting value would be very close to zero. > > The first bracket takes-out the differentially expressed genes between the > mutant subjects at two different time points(21 and 11 minutes) and the > second bracket those between the wild-type subject at the same different > time points. > ..but what differentially expressed genes takes-out the global interaction > contrast? > > In order to evaluate an interaction do I need absolutely the four arrays > in direct comparison done in this example? Not four arrays, but four treatment/sample combinations. You will need replication to compute this contrast. Best, Jim > > Thank you very much for any explaination > > Erika > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
ADD COMMENTlink written 10.2 years ago by James W. MacDonald51k
Dear Jim, thank you for your always usefull explanations. If we observe a gene up-regulated in mutant "class" and also in the wt "class" but the extent of this up-regulation is different and statistically significant, we then should detect this gene as differentially expressed in this contrast...is correct? > Not four arrays, but four treatment/sample combinations. You will need > replication to compute this contrast. > Yes, I know that if I increase the number of contrasts I need more degrees of freedom to compute the statistics. I referred only to direct comparison. If I have more samples and perform a large reference design can I compute this interaction term the same? thank you Erika > Hi Erika, > > Erika Melissari wrote: >> Dear bioconductor list, >> >> I am studing the Weaver experiment example of LIMMA manual and I am in a >> maze about the biological meaning of interaction term present among the >> contrasts. >> I did not manage to understend what kind of differentially expressed >> gene >> this contrast takes-out. > > In this experiment we can look at genes that change between the two time > points in the mutant samples, or that change between the two time points > in the wild type samples. In addition, we might be interested in those > genes that react differently in the two sample types. In other words, a > particular gene might increase expression in the wild type samples, but > actually decrease expression in the mutant samples. > > This third comparison is known as an interaction. > >> The interaction contrast is: >> >> (P21mt-P11mt)-(P21wt-P11wt) > > Correct. So using our example from above, the first term will be > negative (since the expression level went down in mutant samples). The > second term will be positive, since the expression went up over time in > the wild type samples, but since we subtract, we end up with a > (possibly) large negative number. > > The same will be true of any scenario you can envision where the mutant > and wild type samples react differently to the incubation time. Another > example would be the situation where the mutant samples were > up-regulated at 21 hours, but the wild type samples were unaffected. In > this case you can see that we might have a large value for this contrast. > > However, if both wild type and mutant samples were up-regulated > approximately the same amount, the resulting value would be very close > to zero. > >> >> The first bracket takes-out the differentially expressed genes between >> the >> mutant subjects at two different time points(21 and 11 minutes) and the >> second bracket those between the wild-type subject at the same different >> time points. >> ..but what differentially expressed genes takes-out the global >> interaction >> contrast? >> >> In order to evaluate an interaction do I need absolutely the four arrays >> in direct comparison done in this example? > > Not four arrays, but four treatment/sample combinations. You will need > replication to compute this contrast. > > Best, > > Jim > > >> >> Thank you very much for any explaination >> >> Erika >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > Erika Melissari
ADD REPLYlink written 10.2 years ago by Erika Melissari240
Erika Melissari wrote: > Dear Jim, > > thank you for your always usefull explanations. > If we observe a gene up-regulated in mutant "class" and also in the wt > "class" but the extent of this up-regulation is different and > statistically significant, we then should detect this gene as > differentially expressed in this contrast...is correct? If I understand your question correctly, then yes. You can have genes up-regulated in both wt and mutant, but less so in one than the other. If the difference in up-regulation is large enough and the variability within groups is small enough then you should get a significant interaction. Best, Jim > > >> Not four arrays, but four treatment/sample combinations. You will need >> replication to compute this contrast. >> > > Yes, I know that if I increase the number of contrasts I need more degrees > of freedom to compute the statistics. I referred only to direct > comparison. If I have more samples and perform a large reference design > can I compute this interaction term the same? > thank you > > Erika > >> Hi Erika, >> >> Erika Melissari wrote: >>> Dear bioconductor list, >>> >>> I am studing the Weaver experiment example of LIMMA manual and I am in a >>> maze about the biological meaning of interaction term present among the >>> contrasts. >>> I did not manage to understend what kind of differentially expressed >>> gene >>> this contrast takes-out. >> In this experiment we can look at genes that change between the two time >> points in the mutant samples, or that change between the two time points >> in the wild type samples. In addition, we might be interested in those >> genes that react differently in the two sample types. In other words, a >> particular gene might increase expression in the wild type samples, but >> actually decrease expression in the mutant samples. >> >> This third comparison is known as an interaction. >> >>> The interaction contrast is: >>> >>> (P21mt-P11mt)-(P21wt-P11wt) >> Correct. So using our example from above, the first term will be >> negative (since the expression level went down in mutant samples). The >> second term will be positive, since the expression went up over time in >> the wild type samples, but since we subtract, we end up with a >> (possibly) large negative number. >> >> The same will be true of any scenario you can envision where the mutant >> and wild type samples react differently to the incubation time. Another >> example would be the situation where the mutant samples were >> up-regulated at 21 hours, but the wild type samples were unaffected. In >> this case you can see that we might have a large value for this contrast. >> >> However, if both wild type and mutant samples were up-regulated >> approximately the same amount, the resulting value would be very close >> to zero. >> >>> The first bracket takes-out the differentially expressed genes between >>> the >>> mutant subjects at two different time points(21 and 11 minutes) and the >>> second bracket those between the wild-type subject at the same different >>> time points. >>> ..but what differentially expressed genes takes-out the global >>> interaction >>> contrast? >>> >>> In order to evaluate an interaction do I need absolutely the four arrays >>> in direct comparison done in this example? >> Not four arrays, but four treatment/sample combinations. You will need >> replication to compute this contrast. >> >> Best, >> >> Jim >> >> >>> Thank you very much for any explaination >>> >>> Erika >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> > > > > > Erika Melissari > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
ADD REPLYlink written 10.2 years ago by James W. MacDonald51k
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