search for: figurski

...), Visit=rep(c(1:4),10), ProteinA=rnorm(m=10, n=40), ProteinB=rnorm(m=13,s=0.7,n=40)) gls(ProteinB~ProteinA, data=x, corr=corSymm(form=~Visit|Patient.ID) In the results I see correlations between the occasions and between terms, but not between the proteins. Where to look for it? -- Michal J. Figurski, PhD HUP, Pathology & Laboratory Medicine Biomarker Research Laboratory 3400 Spruce St. 7 Maloney S Philadelphia, PA 19104 tel. (215) 662-3413

...o 9000. How do I compare HRs between such variables? I have rescaled all the variables to be in 0 to 1 range - is this the proper way to go? Is there a way to somehow calculate the same HRs (as for rescaled parameters) from the HRs for original parameters? Many thanks in advance. -- Michal J. Figurski, PhD HUP, Pathology & Laboratory Medicine Biomarker Research Laboratory 3400 Spruce St. 7 Maloney Philadelphia, PA 19104 tel. (215) 662-3413

...op with several "if"s, but I was wondering if there is a single function that can do this. I have tried "format", "prettyNum" and "formatC" back and forth, but these functions don't seem to be able to display leading zeros. Please help. -- Michal J. Figurski

...39; throws an error: "Error in summary.survfit(g, print.it = FALSE, times = times) : object 'n.enter' not found" Actually, using 'survest(f, time=3)' has the same result. Has anybody encountered this kind of error? Is there a workaround? Best regards, -- Michal J. Figurski, PhD HUP, Pathology & Laboratory Medicine Biomarker Research Laboratory 3400 Spruce St. 7 Maloney Philadelphia, PA 19104 tel. (215) 662-3413

...d every possible combination of starting values, including the values fitted by the instrument soft - to no avail. I've probably seen all possible error messages from 'nls' trying to fit this. If anyone has an idea why it's not working - let me know. Best regards, -- Michal J. Figurski, PhD HUP, Pathology & Laboratory Medicine Biomarker Research Laboratory 3400 Spruce St. 7 Maloney S Philadelphia, PA 19104 tel. (215) 662-3413

...at", wait=T) the first call runs correctly, but then the second produces and error "The system cannot find the path specified." - completely as if the computer has forgotten all the paths and settings from the first call. Does anyone know a solution to this problem? -- Michal J. Figurski, PhD HUP, Pathology & Laboratory Medicine Biomarker Research Laboratory 3400 Spruce St. 7 Maloney Philadelphia, PA 19104 tel. (215) 662-3413

.... However, I think this is a serious inconvenience, and it should be changed to work in the same way as mean, summary or sd options. Nevertheless, accepting the reality, I have a question to all: how to obtain the by-subject medians of factors in such dataset? Thanks in advance, -- Michal J. Figurski HUP, Pathology & Laboratory Medicine Xenobiotics Toxicokinetics Research Laboratory 3400 Spruce St. 7 Maloney Philadelphia, PA 19104

...pporting the use of bootstrap to determine coefficients, as opposed to just running linear regression on the whole dataset, is the comparison of Rsq and prediction errors between these two approaches - page 1502. There's a substantial difference in favor of the bootstrap approach. -- Michal J. Figurski Gustaf Rydevik wrote: > The url for the mentioned paper is at: > http://www.clinchem.org/cgi/content/full/48/9/1497 > > The bootstrap as applied in that paper is used to evaluate different > regression models against each other (though I wonder how sensible it > is to look at...

...inherent. Nevertheless, I see that the Fig.2 may be incorrect, if we look from orthodox statistical perspective. I used the same plots in my work as well - it's too late now. How should I properly estimate the Rsq then? I greatly appreciate your time and advices in this matter. -- Michal J. Figurski Frank E Harrell Jr wrote: > Gustaf Rydevik wrote: >> On Wed, Jul 23, 2008 at 4:08 PM, Michal Figurski >> <figurski at mail.med.upenn.edu> wrote: >> >> Hi, >> >> I believe that you misunderstand the passage. Do you know what >> multiple stepwise re...

...about 4GB of data... I would like to merge the two datasets and use lmer to build a mixed effects model. Is there a way, for example using 'bigmemory' or 'ff', or any other trick, to enable lmer to work on this data set? I will greatly appreciate any suggestions. -- Michal J. Figurski, PhD HUP, Pathology & Laboratory Medicine Biomarker Research Laboratory 3400 Spruce St. 7 Maloney S Philadelphia, PA 19104 tel. (215) 662-3413

...d it to select _rows_. Though the main point here is the optimized LR equation. I would appreciate any help on how to extract the LR equation coefficients from any of these bootstrap functions, in the same form as given by 'glm' or 'lrm'. Many thanks in advance! -- Michal J. Figurski HUP, Pathology & Laboratory Medicine Xenobiotics Toxicokinetics Research Laboratory 3400 Spruce St. 7 Maloney Philadelphia, PA 19104 tel. (215) 662-3413

...0.01 ?*? 0.05 ?.? 0.1 ? ? 1 Do you guys think this is correct approach? How do I extract these numbers (sum of squares) to store in a separate dataframe for further calculations? And how should I interpret the "Residual" in this setting? I will appreciate your comments. -- Michal J. Figurski

...* Solutions tried: - subtracting SDaa and SDrr from total SD - sometimes produces negative results - adding SDres to SDaa + SDrr is usually greater than total SD - ... I have no idea how to do this in a formally acceptable way. Any help would be appreciated. Kind regards, -- Michal J. Figurski, PhD HUP, Pathology & Laboratory Medicine Biomarker Research Laboratory 3400 Spruce St. 7 Maloney Philadelphia, PA 19104 tel. (215) 662-3413 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Data.csv URL: <https://stat.ethz.ch/pipermail/r-...

...documentation that the 'int' parameter is currently ignored. I guess this means it's not a trivial thing to do. Does anyone have a suggestion on how to obtain confidence predictions for such a model? Please cc my email address when you reply. Thanks and best regards, -- Michal J. Figurski, PhD HUP, Pathology & Laboratory Medicine Biomarker Research Laboratory 3400 Spruce St. 7 Maloney Philadelphia, PA 19104 tel. (215) 662-3413

...(Intercept) Residual StdDev: 3.483794 3.637523 (...) While I have no problem obtaining the 'Residual' value by calling fit$sigma, I have no idea how to obtain the '(Intercept)' value from the 'fit' object. Anyone can help with that? Best regards, -- Michal J. Figurski, PhD HUP, Pathology & Laboratory Medicine Biomarker Research Laboratory 3400 Spruce St. 7 Maloney Philadelphia, PA 19104 tel. (215) 662-3413

...w32 locale: LC_COLLATE=Polish_Poland.1250;LC_CTYPE=Polish_Poland.1250;LC_MONETARY=Polish_Poland.1250;LC_NUMERIC=C;LC_TIME=Polish_Poland.1250 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Cairo_1.4-5 > -- Michal J. Figurski HUP, Pathology & Laboratory Medicine Biomarker Research Laboratory Philadelphia, USA