using mat.samp in siggenes
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@kathleen-kerr-913
Last seen 9.6 years ago
I am using the sam() function in siggenes and I cannot find information about using the option mat.samp: mat.samp: a permutation matrix. If specified, this matrix will be used, even if 'rand' and 'B' are specified. I have a dataset with four treated samples and four control samples that are paired, so my class label is: cl=c(-1,-2,-3,-4, 1,2,3,4) There are only 2^4=16 permutations, so I would just like to enumerate them. The helpfile doesn't give any information about what the permutation matrix should look like. I have tried the matrix with sixteen rows, each of which looks something like c(-1, 2, 3,-4, 1,-2,-3,4) but I get an error message that this is invalid.
siggenes siggenes • 1.1k views
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@james-w-macdonald-5106
Last seen 5 hours ago
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Kathleen Kerr wrote: > I am using the sam() function in siggenes and I > cannot find information about using the option mat.samp: > > mat.samp: a permutation matrix. If specified, this matrix will be used, > even if 'rand' and 'B' are specified. > > I have a dataset with four treated samples and four control samples > that are paired, so my class label is: > cl=c(-1,-2,-3,-4, 1,2,3,4) > > There are only 2^4=16 permutations, so I would just like to enumerate > them. The helpfile doesn't give any information about what the > permutation matrix should look like. The permutation matrix should be a 16 x 4 matrix of 1's and -1's 1 1 1 1 -1 1 1 1 1 -1 1 1 1 1 -1 1 etc HTH, Jim > > I have tried the matrix with sixteen rows, each of which > looks something like > c(-1, 2, 3,-4, 1,-2,-3,4) > but I get an error message that this is invalid. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109
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@holger-schwender-344
Last seen 9.6 years ago
In the next version of siggenes, version 1.2.x, which will (hopefully) be part of Release 1.5 of Bioconductor, it won't be necessary anymore (for a SAM analysis) to specify mat.samp if you wanna do complete permutation since this will be possible by setting B=0 or to an integer equal to or larger than the number of all possible permutations. However, it is still possible to specify mat.samp if you, e.g., would like to use only balanced permutations. Besides from this, there will be many more changes in siggenes since I have rewritten the code for a SAM analysis. E.g., the function sam.plot is replaced by the functions plot and summary, 'data' in sam(...) can be also an exprSet object (using an exprSet object, pData can be used for specifying cl), it is possible to do a two class unpaired analysis assuming *unequal* variances, i.e. an analysis using Welch's t-statistic, a multiclass analysis or an analysis of categorical data such as SNP data, respectively, it is possible to add the locus links to the output, the significant genes are now ordered by their absolute value, i.e. by their "significance", ... The usage of sam will, however, be almost the same -- at least for the "important" arguments. I have only changed the default of med to med=FALSE which means that the mean (and not the median) number of falsely called genes is computed by default. There also will be a manual (hopefully a vignette) which will describe all these changes. Thanks to Kathleen, I will also add a section of how mat.samp has to be specified. I have almost forgotten this. There however will be *no* changes in the empirical Bayes functions. New versions of find.a0, ebam and ebam.wilc with the same features as sam might possibly be part of Release 1.6 of Bioconductor. Sorry for this pretty long mail. I actually only wanted to say that complete permutation is possible in the next version of siggenes. Best, Holger > Kathleen Kerr wrote: > > > I am using the sam() function in siggenes and I > > cannot find information about using the option mat.samp: > > > > mat.samp: a permutation matrix. If specified, this matrix will be used, > > even if 'rand' and 'B' are specified. > > > > I have a dataset with four treated samples and four control samples > > that are paired, so my class label is: > > cl=c(-1,-2,-3,-4, 1,2,3,4) > > > > There are only 2^4=16 permutations, so I would just like to enumerate > > them. The helpfile doesn't give any information about what the > > permutation matrix should look like. > > The permutation matrix should be a 16 x 4 matrix of 1's and -1's > > 1 1 1 1 > -1 1 1 1 > 1 -1 1 1 > 1 1 -1 1 > etc > > HTH, > > Jim > > > > > > > I have tried the matrix with sixteen rows, each of which > > looks something like > > c(-1, 2, 3,-4, 1,-2,-3,4) > > but I get an error message that this is invalid. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Supergünstige DSL-Tarife + WLAN-Router für 0,- EUR* Jetzt zu GMX wechseln und sparen http://www.gmx.net/de/go/dsl
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@kathleen-kerr-913
Last seen 9.6 years ago
Thanks very much for this extended reply. Out of curiosity, does sam() do unbalanced permutations when the data are paired? If so, I suggest that it should default to only doing balanced permutations. By 'balanced' in the paired case, I mean that within each pair the assignment to treatment/control is randomized. Actually, I'm not sure what 'balanced' means in the context of unpaired data. Thanks again, Katie ----- Original Message ----- From: "Holger Schwender" <holger.schw@gmx.de> To: "James W. MacDonald" <jmacdon@med.umich.edu> Cc: <katiek@u.washington.edu>; <bioconductor@stat.math.ethz.ch> Sent: Thursday, September 16, 2004 2:28 AM Subject: Re: [BioC] using mat.samp in siggenes > In the next version of siggenes, version 1.2.x, which will (hopefully) be > part of Release 1.5 of Bioconductor, it won't be necessary anymore (for a > SAM analysis) to specify mat.samp if you wanna do complete permutation since > this will be possible by setting B=0 or to an integer equal to or larger > than the number of all possible permutations. However, it is still possible > to specify mat.samp if you, e.g., would like to use only balanced > permutations. > > Besides from this, there will be many more changes in siggenes since I have > rewritten the code for a SAM analysis. E.g., the function sam.plot is > replaced by the functions plot and summary, 'data' in sam(...) can be also > an exprSet object (using an exprSet object, pData can be used for specifying > cl), it is possible to do a two class unpaired analysis assuming *unequal* > variances, i.e. an analysis using Welch's t-statistic, a multiclass analysis > or an analysis of categorical data such as SNP data, respectively, it is > possible to add the locus links to the output, the significant genes are now > ordered by their absolute value, i.e. by their "significance", ... > > The usage of sam will, however, be almost the same -- at least for the > "important" arguments. I have only changed the default of med to med=FALSE > which means that the mean (and not the median) number of falsely called > genes is computed by default. > > There also will be a manual (hopefully a vignette) which will describe all > these changes. Thanks to Kathleen, I will also add a section of how mat.samp > has to be specified. I have almost forgotten this. > > There however will be *no* changes in the empirical Bayes functions. New > versions of find.a0, ebam and ebam.wilc with the same features as sam might > possibly be part of Release 1.6 of Bioconductor. > > Sorry for this pretty long mail. I actually only wanted to say that complete > permutation is possible in the next version of siggenes. > > Best, > Holger > > > > > Kathleen Kerr wrote: > > > > > I am using the sam() function in siggenes and I > > > cannot find information about using the option mat.samp: > > > > > > mat.samp: a permutation matrix. If specified, this matrix will be used, > > > even if 'rand' and 'B' are specified. > > > > > > I have a dataset with four treated samples and four control samples > > > that are paired, so my class label is: > > > cl=c(-1,-2,-3,-4, 1,2,3,4) > > > > > > There are only 2^4=16 permutations, so I would just like to enumerate > > > them. The helpfile doesn't give any information about what the > > > permutation matrix should look like. > > > > The permutation matrix should be a 16 x 4 matrix of 1's and -1's > > > > 1 1 1 1 > > -1 1 1 1 > > 1 -1 1 1 > > 1 1 -1 1 > > etc > > > > HTH, > > > > Jim > > > > > > > > > > > > I have tried the matrix with sixteen rows, each of which > > > looks something like > > > c(-1, 2, 3,-4, 1,-2,-3,4) > > > but I get an error message that this is invalid. > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > -- > > James W. MacDonald > > Affymetrix and cDNA Microarray Core > > University of Michigan Cancer Center > > 1500 E. Medical Center Drive > > 7410 CCGC > > Ann Arbor MI 48109 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > -- > Superg?nstige DSL-Tarife + WLAN-Router f?r 0,- EUR* > Jetzt zu GMX wechseln und sparen http://www.gmx.net/de/go/dsl > >
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@holger-schwender-344
Last seen 9.6 years ago
In the unpaired case, a balanced permutation is a permutation of the group labels such that each group contains the same number of samples from each of the original groups. So if each of the 2 groups contain n samples, then in a balanced permutation, each group contains n/2 samples from group 1 and n/2 samples from group 2. If it is not possible to get balanced permutations, they should be at least as balanced as possible -- what ever this means. The argument bal for balanced permutations which can actually only be used in the unpaired case will be removed in the next version of siggenes. If I understand you correctly, sam uses what you call balanced permutations in the paired case. Best, Holger > Thanks very much for this extended reply. > Out of curiosity, does sam() do unbalanced > permutations when the data are paired? If so, > I suggest that it should default to only > doing balanced permutations. By 'balanced' > in the paired case, I mean that within each pair > the assignment to treatment/control is randomized. > Actually, I'm not sure what 'balanced' means in the context > of unpaired data. > > Thanks again, > Katie > > ----- Original Message ----- > From: "Holger Schwender" <holger.schw@gmx.de> > To: "James W. MacDonald" <jmacdon@med.umich.edu> > Cc: <katiek@u.washington.edu>; <bioconductor@stat.math.ethz.ch> > Sent: Thursday, September 16, 2004 2:28 AM > Subject: Re: [BioC] using mat.samp in siggenes > > > > In the next version of siggenes, version 1.2.x, which will (hopefully) > be > > part of Release 1.5 of Bioconductor, it won't be necessary anymore (for > a > > SAM analysis) to specify mat.samp if you wanna do complete permutation > since > > this will be possible by setting B=0 or to an integer equal to or larger > > than the number of all possible permutations. However, it is still > possible > > to specify mat.samp if you, e.g., would like to use only balanced > > permutations. > > > > Besides from this, there will be many more changes in siggenes since I > have > > rewritten the code for a SAM analysis. E.g., the function sam.plot is > > replaced by the functions plot and summary, 'data' in sam(...) can be > also > > an exprSet object (using an exprSet object, pData can be used for > specifying > > cl), it is possible to do a two class unpaired analysis assuming > *unequal* > > variances, i.e. an analysis using Welch's t-statistic, a multiclass > analysis > > or an analysis of categorical data such as SNP data, respectively, it is > > possible to add the locus links to the output, the significant genes are > now > > ordered by their absolute value, i.e. by their "significance", ... > > > > The usage of sam will, however, be almost the same -- at least for the > > "important" arguments. I have only changed the default of med to > med=FALSE > > > which means that the mean (and not the median) number of falsely called > > genes is computed by default. > > > > There also will be a manual (hopefully a vignette) which will describe > all > > these changes. Thanks to Kathleen, I will also add a section of how > mat.samp > > has to be specified. I have almost forgotten this. > > > > There however will be *no* changes in the empirical Bayes functions. New > > versions of find.a0, ebam and ebam.wilc with the same features as sam > might > > possibly be part of Release 1.6 of Bioconductor. > > > > Sorry for this pretty long mail. I actually only wanted to say that > complete > > permutation is possible in the next version of siggenes. > > > > Best, > > Holger > > > > > > > > > Kathleen Kerr wrote: > > > > > > > I am using the sam() function in siggenes and I > > > > cannot find information about using the option mat.samp: > > > > > > > > mat.samp: a permutation matrix. If specified, this matrix will be > used, > > > > even if 'rand' and 'B' are specified. > > > > > > > > I have a dataset with four treated samples and four control samples > > > > that are paired, so my class label is: > > > > cl=c(-1,-2,-3,-4, 1,2,3,4) > > > > > > > > There are only 2^4=16 permutations, so I would just like to > enumerate > > > > them. The helpfile doesn't give any information about what the > > > > permutation matrix should look like. > > > > > > The permutation matrix should be a 16 x 4 matrix of 1's and -1's > > > > > > 1 1 1 1 > > > -1 1 1 1 > > > 1 -1 1 1 > > > 1 1 -1 1 > > > etc > > > > > > HTH, > > > > > > Jim > > > > > > > > > > > > > > > > > I have tried the matrix with sixteen rows, each of which > > > > looks something like > > > > c(-1, 2, 3,-4, 1,-2,-3,4) > > > > but I get an error message that this is invalid. > > > > > > > > _______________________________________________ > > > > Bioconductor mailing list > > > > Bioconductor@stat.math.ethz.ch > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > > -- > > > James W. MacDonald > > > Affymetrix and cDNA Microarray Core > > > University of Michigan Cancer Center > > > 1500 E. Medical Center Drive > > > 7410 CCGC > > > Ann Arbor MI 48109 > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > -- > > Superg?nstige DSL-Tarife + WLAN-Router f?r 0,- EUR* > > Jetzt zu GMX wechseln und sparen http://www.gmx.net/de/go/dsl > > > > > -- Superg?nstige DSL-Tarife + WLAN-Router f?r 0,- EUR* Jetzt zu GMX wechseln und sparen http://www.gmx.net/de/go/dsl
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