affycoretools: group parameter
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@ingrid-h-g-stensen-1971
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@james-w-macdonald-5106
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Hi Ingrid, Ingrid H. G. ?stensen wrote: > Hi > > I have an experiment with 24 cel files divided into 6 groups (4 of > each type). In affycoretools the group parameter would be like this: > groups = rep(1:24, each = 4). > > After the QC I found out that one of the arrays was really bad and > had to be removed. In other words there are now 5 groups with 4 > arrays and one with 3 arrays. What should I put in the group > parameter now? I have tried different things but nothing has worked > so far. The groups argument (not a parameter) you are specifying isn't correct to begin with. You want groups = rep(1:6, each = 4). The groups argument you are specifying now is a numeric vector of length 96, instead of length 24. I should probably put in some error checking to prevent mis-specified groups arguments. Anyway, the groups argument just specifies what group each celfile belongs to, so you can simply subset the correct argument to remove one of the replicates for the group that has been reduced. For instance, let's say you removed the third replicate of the fourth group. You can then specify the groups argument like this: groups = rep(1:6, each=4)[-14] Best, Jim > > Regards, Ingrid > > > > > [[alternative HTML version deleted]] > > _______________________________________________ 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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Ingrid H. G. ?stensen wrote: > Hi > > Why is it [-14] and not [-15]? Is the group parameter zero based? Actually I was completely off. The third replicate of the fourth group would be the 12th member of the vector, so you want [-12]. Although any of [-10], [-11], [-12] would result in the same thing, as all you want to do is end up with a groups vector that looks like 1 1 1 2 2 2 3 3 3 4 4 5 5 5 6 6 6 So removing any of the 4s will give you what you want. Sorry for the confusion. Best, Jim > > Regards, > Ingrid > > > > > > Hi Ingrid, > > Ingrid H. G. ?stensen wrote: > >>Hi >> >>I have an experiment with 24 cel files divided into 6 groups (4 of >>each type). In affycoretools the group parameter would be like this: >>groups = rep(1:24, each = 4). >> >>After the QC I found out that one of the arrays was really bad and >>had to be removed. In other words there are now 5 groups with 4 >>arrays and one with 3 arrays. What should I put in the group >>parameter now? I have tried different things but nothing has worked >>so far. > > > The groups argument (not a parameter) you are specifying isn't correct > to begin with. You want groups = rep(1:6, each = 4). The groups argument > you are specifying now is a numeric vector of length 96, instead of > length 24. I should probably put in some error checking to prevent > mis-specified groups arguments. > > Anyway, the groups argument just specifies what group each celfile > belongs to, so you can simply subset the correct argument to remove one > of the replicates for the group that has been reduced. For instance, > let's say you removed the third replicate of the fourth group. You can > then specify the groups argument like this: > > groups = rep(1:6, each=4)[-14] > > Best, > > Jim > > > > >>Regards, Ingrid >> >> >> >> >>[[alternative HTML version deleted]] >> >>_______________________________________________ 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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groups <- lapply(1:6, rep, each=4) groups[[4]] <- groups[[4]][-1] # Remove one from 4th group groups <- unlist(groups) /HB On 2/19/07, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Ingrid H. G. ?stensen wrote: > > Hi > > > > Why is it [-14] and not [-15]? Is the group parameter zero based? > > Actually I was completely off. The third replicate of the fourth group > would be the 12th member of the vector, so you want [-12]. Although any > of [-10], [-11], [-12] would result in the same thing, as all you want > to do is end up with a groups vector that looks like > > 1 1 1 2 2 2 3 3 3 4 4 5 5 5 6 6 6 > > So removing any of the 4s will give you what you want. > > Sorry for the confusion. > > Best, > > Jim > > > > > > Regards, > > Ingrid > > > > > > > > > > > > Hi Ingrid, > > > > Ingrid H. G. ?stensen wrote: > > > >>Hi > >> > >>I have an experiment with 24 cel files divided into 6 groups (4 of > >>each type). In affycoretools the group parameter would be like this: > >>groups = rep(1:24, each = 4). > >> > >>After the QC I found out that one of the arrays was really bad and > >>had to be removed. In other words there are now 5 groups with 4 > >>arrays and one with 3 arrays. What should I put in the group > >>parameter now? I have tried different things but nothing has worked > >>so far. > > > > > > The groups argument (not a parameter) you are specifying isn't correct > > to begin with. You want groups = rep(1:6, each = 4). The groups argument > > you are specifying now is a numeric vector of length 96, instead of > > length 24. I should probably put in some error checking to prevent > > mis-specified groups arguments. > > > > Anyway, the groups argument just specifies what group each celfile > > belongs to, so you can simply subset the correct argument to remove one > > of the replicates for the group that has been reduced. For instance, > > let's say you removed the third replicate of the fourth group. You can > > then specify the groups argument like this: > > > > groups = rep(1:6, each=4)[-14] > > > > Best, > > > > Jim > > > > > > > > > >>Regards, Ingrid > >> > >> > >> > >> > >>[[alternative HTML version deleted]] > >> > >>_______________________________________________ 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 > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. > > _______________________________________________ > 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
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