request for letter of support
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 9.6 years ago
United States
Hi folks, Some of us are in the process of submitting a grant proposal to fund aspects of the Bioconductor project. We would like to get letters of support from individuals that are using or plan to use Bioconductor software. If you could address them to me, and send them to: Dr. R. Gentleman Dept. of Biostatistical Science DFCI 44 Binney St. Boston, Ma USA 02115 As is usually the case, I have left this later than planned. I need them here by the 22nd of this month -- so if you are going to do it, please do it soon. Please use company or University letter head. If the deadline is too tight please fax me the letter (although an original is preferable) -- number is below. Thanks in advance, Robert -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+
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@hinnerk-boriss-111
Last seen 10.2 years ago
Hi there! I have a statement like this: data.lwf <- express(data, summary.stat=li.wong) and I get the following error message: Error in data.matrix[,!phi.outliers] %*% phi[!phi.outliers] : non-conformable arguments What does this error message mean in detail? Does the li.wong routine require to do some outlier checking beforehand? If so, what method is approporiate? Just to mention, I am not a fan of removing outliers. Anyway, How would I find the trouble making values in my data? Cheers, Hinnerk
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my guess is that one of those guys was left with just one column (or none) and was turned into a vector. we probably need to add a drop=FALSE somewhere. On Wed, 13 Nov 2002, Hinnerk Boriss wrote: > Hi there! > > I have a statement like this: > > data.lwf <- express(data, summary.stat=li.wong) > > and I get the following error message: > > Error in data.matrix[,!phi.outliers] %*% phi[!phi.outliers] : > non-conformable arguments > > What does this error message mean in detail? Does the li.wong routine > require to do some outlier checking beforehand? If so, what method is > approporiate? Just to mention, I am not a fan of removing outliers. > Anyway, How would I find the trouble making values in my data? > > Cheers, > Hinnerk > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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I think that error message is what I got in using an Hu6800 chip where there are (apparently) two probe sets with just one pair. The hack I used was to insert after this line in fit.li.wong: J <- dim(data.matrix)[2] the following comment and line: ### The following line is intended to deal with a problem in the ### treatment of Hu6800 chips. That chip has a couple of probe sets ### in which there is only one PM-MM pair. Probably, it is just a ### control region, so I am omitting the fit.li.wong operations for ### any such probe set if (J == 1) return(list(theta=c(data.matrix),sigma.theta=rep(NA,len gth(data.matrix)))) On Wed, 13 Nov 2002, Rafael A. Irizarry wrote: > my guess is that one of those guys was left with just one column (or > none) and was turned into a vector. we probably need to add a drop=FALSE > somewhere. > > On Wed, 13 Nov 2002, Hinnerk Boriss wrote: > > > Hi there! > > > > I have a statement like this: > > > > data.lwf <- express(data, summary.stat=li.wong) > > > > and I get the following error message: > > > > Error in data.matrix[,!phi.outliers] %*% phi[!phi.outliers] : > > non-conformable arguments > > > > What does this error message mean in detail? Does the li.wong routine > > require to do some outlier checking beforehand? If so, what method is > > approporiate? Just to mention, I am not a fan of removing outliers. > > Anyway, How would I find the trouble making values in my data? > > > > Cheers, > > Hinnerk > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > Charles C. Berry (858) 534-2098 Dept of Family/Preventive Medicine E mailto:cberry@tajo.ucsd.edu UC San Diego http://hacuna.ucsd.edu/members/ccb.html La Jolla, San Diego 92093-0645
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Yes, I do work with Hu6800 chips and thanks, I get past that error message, however, I run into a new one: Error in apply(resid[, !phi.outliers]^2, 1, sum) : dim(x) must have a positive length > traceback() 8: stop("dim(X) must have a positive length") 7: apply(resid[, !phi.outliers]^2, 1, sum) 6: fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile, normal.resid.quantile, large.threshold, large.variation, outlier.fraction, delta, maxit, outer.maxit, verbose) 5: FUN(X[[4318]], ...) 4: lapply(as.list(X), FUN, ...) 3: sapply(data.lst, summary.stat, ...) 2: t(sapply(data.lst, summary.stat, ...)) 1: express(NormLemonData, summary.stat = li.wong) Any suggestions on that one? Cheers, Hinnerk > > I think that error message is what I got in using an Hu6800 chip where > there are (apparently) two probe sets with just one pair. The > hack I used > was to insert after this line in fit.li.wong: > > J <- dim(data.matrix)[2] > > the following comment and line: > > ### The following line is intended to deal with a problem in the > ### treatment of Hu6800 chips. That chip has a couple of probe sets > ### in which there is only one PM-MM pair. Probably, it is just a > ### control region, so I am omitting the fit.li.wong operations for > ### any such probe set > > if (J == 1) > return(list(theta=c(data.matrix),sigma.theta=rep(NA,length(dat a.matrix)))) > > > > On Wed, 13 Nov 2002, Rafael A. Irizarry wrote: > > > my guess is that one of those guys was left with just one > column (or > > none) and was turned into a vector. we probably need to add > a drop=FALSE > > somewhere. > > > > On Wed, 13 Nov 2002, Hinnerk Boriss wrote: > > > > > Hi there! > > > > > > I have a statement like this: > > > > > > data.lwf <- express(data, summary.stat=li.wong) > > > > > > and I get the following error message: > > > > > > Error in data.matrix[,!phi.outliers] %*% phi[!phi.outliers] : > > > non-conformable arguments > > > > > > What does this error message mean in detail? Does the > li.wong routine > > > require to do some outlier checking beforehand? If so, > what method is > > > approporiate? Just to mention, I am not a fan of removing > outliers. > > > Anyway, How would I find the trouble making values in my data? > > > > > > Cheers, > > > Hinnerk > > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > Charles C. Berry (858) 534-2098 > Dept of > Family/Preventive Medicine > E mailto:cberry@tajo.ucsd.edu UC San Diego > http://hacuna.ucsd.edu/members/ccb.html La Jolla, San Diego > 92093-0645 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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i think the hg6800 chip has a one probe probe set which makes li.wong break down. On Thu, 14 Nov 2002, Hinnerk Boriss wrote: > Yes, I do work with Hu6800 chips and thanks, I get past that error > message, however, I run into a new one: > Error in apply(resid[, !phi.outliers]^2, 1, sum) : > dim(x) must have a positive length > > > traceback() > 8: stop("dim(X) must have a positive length") > 7: apply(resid[, !phi.outliers]^2, 1, sum) > 6: fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile, > normal.resid.quantile, large.threshold, large.variation, > outlier.fraction, delta, maxit, outer.maxit, verbose) > 5: FUN(X[[4318]], ...) > 4: lapply(as.list(X), FUN, ...) > 3: sapply(data.lst, summary.stat, ...) > 2: t(sapply(data.lst, summary.stat, ...)) > 1: express(NormLemonData, summary.stat = li.wong) > > > Any suggestions on that one? > > Cheers, > Hinnerk > > > > > > I think that error message is what I got in using an Hu6800 chip where > > there are (apparently) two probe sets with just one pair. The > > hack I used > > was to insert after this line in fit.li.wong: > > > > J <- dim(data.matrix)[2] > > > > the following comment and line: > > > > ### The following line is intended to deal with a problem in the > > ### treatment of Hu6800 chips. That chip has a couple of probe sets > > ### in which there is only one PM-MM pair. Probably, it is just a > > ### control region, so I am omitting the fit.li.wong operations for > > ### any such probe set > > > > if (J == 1) > > return(list(theta=c(data.matrix),sigma.theta=rep(NA,length(dat > a.matrix)))) > > > > > > > > On Wed, 13 Nov 2002, Rafael A. Irizarry wrote: > > > > > my guess is that one of those guys was left with just one > > column (or > > > none) and was turned into a vector. we probably need to add > > a drop=FALSE > > > somewhere. > > > > > > On Wed, 13 Nov 2002, Hinnerk Boriss wrote: > > > > > > > Hi there! > > > > > > > > I have a statement like this: > > > > > > > > data.lwf <- express(data, summary.stat=li.wong) > > > > > > > > and I get the following error message: > > > > > > > > Error in data.matrix[,!phi.outliers] %*% phi[!phi.outliers] : > > > > non-conformable arguments > > > > > > > > What does this error message mean in detail? Does the > > li.wong routine > > > > require to do some outlier checking beforehand? If so, > > what method is > > > > approporiate? Just to mention, I am not a fan of removing > > outliers. > > > > Anyway, How would I find the trouble making values in my data? > > > > > > > > Cheers, > > > > Hinnerk > > > > > > > > > > > > _______________________________________________ > > > > Bioconductor mailing list > > > > Bioconductor@stat.math.ethz.ch > > > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > Charles C. Berry (858) 534-2098 > > Dept of > > Family/Preventive Medicine > > E mailto:cberry@tajo.ucsd.edu UC San Diego > > http://hacuna.ucsd.edu/members/ccb.html La Jolla, San Diego > > 92093-0645 > > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > >
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It does. But the patch I suggested got Hinnerk past the first one (1127 in sequence). 4318 appears to be "U34301_at" which has 2 probe sets. On Thu, 14 Nov 2002, Rafael A. Irizarry wrote: > i think the hg6800 chip has a one probe probe set which makes li.wong > break down. > > On Thu, 14 Nov 2002, Hinnerk Boriss wrote: > > > Yes, I do work with Hu6800 chips and thanks, I get past that error > > message, however, I run into a new one: > > Error in apply(resid[, !phi.outliers]^2, 1, sum) : > > dim(x) must have a positive length > > > > > traceback() > > 8: stop("dim(X) must have a positive length") > > 7: apply(resid[, !phi.outliers]^2, 1, sum) > > 6: fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile, > > normal.resid.quantile, large.threshold, large.variation, > > outlier.fraction, delta, maxit, outer.maxit, verbose) > > 5: FUN(X[[4318]], ...) > > 4: lapply(as.list(X), FUN, ...) > > 3: sapply(data.lst, summary.stat, ...) > > 2: t(sapply(data.lst, summary.stat, ...)) > > 1: express(NormLemonData, summary.stat = li.wong) > > > > > > Any suggestions on that one? > > > > Cheers, > > Hinnerk > > > > > > > > > > I think that error message is what I got in using an Hu6800 chip where > > > there are (apparently) two probe sets with just one pair. The > > > hack I used > > > was to insert after this line in fit.li.wong: > > > > > > J <- dim(data.matrix)[2] > > > > > > the following comment and line: > > > > > > ### The following line is intended to deal with a problem in the > > > ### treatment of Hu6800 chips. That chip has a couple of probe sets > > > ### in which there is only one PM-MM pair. Probably, it is just a > > > ### control region, so I am omitting the fit.li.wong operations for > > > ### any such probe set > > > > > > if (J == 1) > > > return(list(theta=c(data.matrix),sigma.theta=rep(NA,length(dat > > a.matrix)))) > > > > > > > > > > > > On Wed, 13 Nov 2002, Rafael A. Irizarry wrote: > > > > > > > my guess is that one of those guys was left with just one > > > column (or > > > > none) and was turned into a vector. we probably need to add > > > a drop=FALSE > > > > somewhere. > > > > > > > > On Wed, 13 Nov 2002, Hinnerk Boriss wrote: > > > > > > > > > Hi there! > > > > > > > > > > I have a statement like this: > > > > > > > > > > data.lwf <- express(data, summary.stat=li.wong) > > > > > > > > > > and I get the following error message: > > > > > > > > > > Error in data.matrix[,!phi.outliers] %*% phi[!phi.outliers] : > > > > > non-conformable arguments > > > > > > > > > > What does this error message mean in detail? Does the > > > li.wong routine > > > > > require to do some outlier checking beforehand? If so, > > > what method is > > > > > approporiate? Just to mention, I am not a fan of removing > > > outliers. > > > > > Anyway, How would I find the trouble making values in my data? > > > > > > > > > > Cheers, > > > > > Hinnerk > > > > > > > > > > > > > > > _______________________________________________ > > > > > Bioconductor mailing list > > > > > Bioconductor@stat.math.ethz.ch > > > > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > > > > > > _______________________________________________ > > > > Bioconductor mailing list > > > > Bioconductor@stat.math.ethz.ch > > > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > > > Charles C. Berry (858) 534-2098 > > > Dept of > > > Family/Preventive Medicine > > > E mailto:cberry@tajo.ucsd.edu UC San Diego > > > http://hacuna.ucsd.edu/members/ccb.html La Jolla, San Diego > > > 92093-0645 > > > > > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > Charles C. Berry (858) 534-2098 Dept of Family/Preventive Medicine E mailto:cberry@tajo.ucsd.edu UC San Diego http://hacuna.ucsd.edu/members/ccb.html La Jolla, San Diego 92093-0645
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