[R] Finding matches in 2 files

I have 2 files containing data analysed by 2 different methods. I would like to find out which genes appear in both analyses. Can someone show me how to do this? _ [[trailing spam removed]] [[alternative HTML version

Re: [R] qda(MASS) function error

Mauro Rossi wrote: Dear R user, I'm using qda (quadratic discriminant analysis) function (package MASS) to classify 58 explanatory variables (numeric type with different ranges) using a grouping variable (factor 2 levels 0 1). I'm using the qda method for class 'data.frame' (in this way

Re: [R] Finding matches in 2 files

Maybe 'merge', but your message is wa First On 7/26/07, jenny tan [EMAIL PROTECTED] wrote: I have 2 files containing data analysed by 2 different methods. I would like to find out which genes appear in both analyses. Can someone show me how to do this?

Re: [R] Finding matches in 2 files

Maybe with 'merge', but your message is too vague (see http://www.catb.org/~esr/faqs/smart-questions.html). On 7/26/07, jenny tan [EMAIL PROTECTED] wrote: I have 2 files containing data analysed by 2 different methods. I would like to find out which genes appear in both analyses. Can someone

Re: [R] For loops

Any time you are calling a function one value at a time, it is worth asking if you can eliminate a loop (or more). If 'G.fun' is vectorized in its first argument, then you can easily get rid of the three inner loops. Just generate a vector of all of the values and do: gj -

Re: [R] ROC curve in R

You might also want to try the ROCR package (http://rocr.bioinf.mpi-sb.mpg.de/). Tutorial slides: http://rocr.bioinf.mpi-sb.mpg.de/ROCR_Talk_Tobias_Sing.ppt Overview paper: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/20/3940 Good luck, Tobias On 7/26/07, Rithesh M. Mohan

[R] Submatrices Extraction

Hello, Given a submatrix containing 0 or 1 I need to extract the indexes of all the diagonal submatrices so one of the two diagonals must contains only 1 for each submatrix ... Any help? Thanks in advance Bruno -- Scegli infostrada: ADSL

[R] Regression with Missing values. na.action?

Hi all, Can you please tell me what is the problem here. My regression eq is y = B0 + B1X1 +B2X2 +e And i am interested in coefficient B1 I am doing regression with two cases: 1) reg-lm(y ~ X1 + X2, sam) where sam is the data 2) reg-lm(y ~ X1 + X2, sam, na.action= na.exclude) . I have

Re: [R] Regression with Missing values. na.action?

na.exclude should give the same results as na.omit, which is the default na.action. Is the number of complete cases the same in these two regressions? On 26/07/07, Vaibhav Gathibandhe [EMAIL PROTECTED] wrote: Hi all, Can you please tell me what is the problem here. My regression eq is y =

Re: [R] Finding matches in 2 files

Something like: # Sample data g1-c(gene1, gene2, gene3, gene4, gene5, gene9, gene10, geneA) g2-c(gene6, gene9, gene1, gene2, gene7, gene8, gene9, gene1, gene10) df1-cbind(gene=g1, expr=runif(length(g1))) df2-cbind(gene=g2, expr=runif(length(g2))) # Merge mdf-merge(df1, df2, by=gene, sort=T) #

[R] Download multiple stock quotes in a loop

Hi all, this should be a simple question, but I haven't been able to do it right. I am trying to download multiple stock quotes in a loop, so that every timeseries is safed with the symbol of the stock. Can anybody help me out? Here's the code: require(tseries) startd - 2000-06-01 stocks -

Re: [R] Download multiple stock quotes in a loop

Owe Jessen wrote: Hi all, this should be a simple question, but I haven't been able to do it right. I am trying to download multiple stock quotes in a loop, so that every timeseries is safed with the symbol of the stock. Can anybody help me out? Here's the code: require(tseries)

Re: [R] Finding matches in 2 files

Is this what you want? g1-c(gene1, gene2, gene3, gene4, gene5, gene9, gene10, + geneA) g2-c(gene6, gene9, gene1, gene2, gene7, gene8, gene9, + gene1, gene10) intersect(g1,g2) [1] gene1 gene2 gene9 gene10 On 7/25/07, jenny tan [EMAIL PROTECTED] wrote: I have 2 files containing data

[R] multiple graphs

Does anyone have a simple explanation and example on how to add histograms or barcharts to an other graph like in the example at the R-graph gallery: http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=109 looking at the code I'not undertand very well how to add graphs in

[R] logistic regression

Greetings, I am working on a logistic regression model in R and I am struggling with the code, as it is a relatively new program for me. In searching Google for 'logistic regression diagnostics' I came Elizabeth Brown's Lecture 14 from her Winter 2004 Biostatistics 515 course

Re: [R] substituting dots in the names of the columns (sub, gsub, regexpr)

Use \\. or [.] with quotes to denote a literal dot (#1) or can use fixed = TRUE to remove the meaning of dot (#2) or use a zero-width lookahead assertion (?=[.]) which will be matched but is not added to the string to be replaced (#3). Try ?regexpr . Also the links on the gsubfn home page

Re: [R] substituting dots in the names of the columns (sub, gsub, regexpr)

Use \\. or [.] with quotes to denote a literal dot (#1) or can use fixed = TRUE to remove the meaning of dot (#2) or use a zero-width lookahead assertion (?=[.]) which will be matched but is not added to the string to be replaced (#3). Try ?regexpr . Also the links on the gsubfn home page

[R] Fit t Copula

Hi, I am trying to fit t copula to some data, and I am using the following function in the library(QRMlib). Udatac - apply(datac, 2, edf,adjust=1) tcopulac - fit.tcopula.rank(Udatac) But the error message come out Error in fit.tcopula.rank(Udatac) : Non p.s.d. covariance matrix Could anyone

Re: [R] Create Strings of Column Id's

Is this what you want: paste(-, paste(colnames(MyMatrix)[COL], collapse='-'), sep='') [1] -E-T On 7/26/07, Tom.O [EMAIL PROTECTED] wrote: Does anyone know how this is don? I have a large matrix where I extract specific columns into txt files for further use. To be able to keep track of

Re: [R] Help with Dates

Are you using the latest version of fame? 1.05 and earlier had a bug in tisFromCsv that was fixed in 1.08. Below I show what I get with fame version 1.08. There is still a problem in that the frequency-figuring logic appears to think the frequency is bwsunday (biweekly with weeks ending on

Re: [R] How to auto-scale cex of y-axis labels in lattice dotplot?

On 7/25/07, Kevin Wright [EMAIL PROTECTED] wrote: When I create a dotplot in lattice, I frequently observe overplotting of the labels along the vertical axis. On my screen, this illustrates overplotting of the letters: windows() reps=6 dat=data.frame(let=rep(letters,each=reps),

Re: [R] Constructing bar charts with standard error bars

John Zabroski wrote: On 7/25/07, Ben Bolker [EMAIL PROTECTED] wrote: Thanks a lot! I tried all three and they all seem very dependable. Also, I appreciate you rewriting my solution and adding elegance. Is there a way to extend the tick marks to the ylim values, such that the yscale ymax

[R] offset in coxph

The offset argument used in glm and other functions seems to have been removed from the argument list for coxph. I am wondering if there is a reason for this and if there is a possible work-around in order to produce a cox-ph object without fitting coefficients? Thanks, Mike

Re: [R] R CMD check sh: line 1: make: command not found

On Thu, 26 Jul 2007, David Peltier wrote: hello, I am using R 2.5.0 under OS X. I am having sh: line 1: make: command not found error message when I run R CMD check : Any help would be appreciated. Well, that is easy: 'make' is missing. It should be there in the OS, so you need to

Re: [R] Convert string to list?

Is this what you want: str - P = 0.0, T = 0.0, Q = 0.0 x - eval(parse(text=paste('list(', str, ')'))) str(x) List of 3 $ P: num 0 $ T: num 0 $ Q: num 0 On 7/26/07, Manuel Morales [EMAIL PROTECTED] wrote: Let's say I have the following string: str - P = 0.0, T = 0.0, Q = 0.0 I'd like

Re: [R] Convert string to list?

Manuel Jim's may be what you want-- a list of numerics with names P, T and Q or a list of character strings? str - P = 0.0, T = 0.0, Q = 0.0 str(as.vector(unlist(strsplit(str,,)),mode=list)) List of 3 $ : chr P = 0.0 $ : chr T = 0.0 $ : chr Q = 0.0 -Original Message- From:

Re: [R] Minitab Parametric Distribution Analysis in R

After a bit of coaching I found what I was looking for: the fitdistr() function in the MASS package. It appears to be a bit easier to use than mle() for my application. Thanks all. Tom -Original Message- From: Thomas Lumley [mailto:[EMAIL PROTECTED] Sent: Wednesday, July 25, 2007 12:03

[R] Convert string to list?

Let's say I have the following string: str - P = 0.0, T = 0.0, Q = 0.0 I'd like to find a function that generates the following object from 'str'. list(P = 0.0, T = 0.0, Q = 0.0) Thanks! -- http://mutualism.williams.edu __ R-help@stat.math.ethz.ch

[R] Survival analysis with 60% random censoring

Hello, My study is to predict the likelihood an insurance policy holder will not renew his policy in the coming expiration date. My data has about 60% censoring and they are random, because customers buy insurance at different time, however, the study has to be terminated on a single date. Any

Re: [R] offset in coxph

Removed? That it was ever there is not my recollection and seems very unlikely given that survival is ported from S where glm() does not have it, As far as I know it has only ever been in glm() and lm() in R: the way which is described in the White Book is to use the offset() function, and

[R] Creating a cross table out of a large dataset

Dear all, I want to make a cross table out of a data set which is 2 columns wide and more than 15 rows long. When I use the table() function I get an error message This is the code I have used: Dataset - read.table(test.txt, header=TRUE, sep=,, na.strings=NA, dec=., strip.white=TRUE) .T

[R] R CMD check sh: line 1: make: command not found

hello, I am using R 2.5.0 under OS X. I am having sh: line 1: make: command not found error message when I run R CMD check : Any help would be appreciated. R CMD check backtest * checking for working latex ... OK * using log directory '/backtest/trunk/backtest.Rcheck' * using R version

Re: [R] Function to separate effect in AOV

You may want to look at the interaction function (a quick way to make the single factor with 4 levels that you mention). You can create your own sets of contrasts and set them using the C or contrasts functions, then use the split argument to summary.aov to look at the individual degrees of

[R] Create Strings of Column Id's

Does anyone know how this is don? I have a large matrix where I extract specific columns into txt files for further use. To be able to keep track of which txt files contain which columns I want to name the filenames with the column Id's. The most basic example would be to use an for() loop

[R] Large dataset + randomForest

[Please CC me in any replies as I am not currently subscribed to the list. Thanks!] Dear all, I did a bit of searching on the question of large datasets but did not come to a definite conclusion. What I am trying to do is the following: I want to read in a dataset with approx. 100 000 rows

[R] zeroinfl() or zicounts() error

I'm trying to fit a zero-inflated poisson model using zeroinfl() from the pscl library. It works fine for most models I try, but when I include either of 2 covariates, I get an error. When I include PopulationDensity, I get this error: Error in solve.default (as.matrix(fit$hessian)) :

Re: [R] Redirecting print output

You may want to look at the R2HTML package as one approach (others have already told you about sink and cat). Another approach is to use the variations on sweave. Here you set up a template file with the code you want run as well as any explanitory text (you can even write an entire report),

Re: [R] multiple graphs

One of the nice things about the R Graph Gallery is that if you click on the R logo underneath the graph (may need to scroll down a bit) it will show you the code used to create that particular graph. You may also want to look at the subplot function in the TeachingDemos package for another way

Re: [R] Help with Dates

Yes, I was using 1.05. I get the same result as you with 1.08. On 26 Jul 2007 11:39:41 -0400, Jeffrey J. Hallman [EMAIL PROTECTED] wrote: Are you using the latest version of fame? 1.05 and earlier had a bug in tisFromCsv that was fixed in 1.08. Below I show what I get with fame version

Re: [R] significance test for difference of two correlations

Let r_1 be the correlation between the two variables for the first group with n_1 subjects and let r_2 be the correlation for the second group with n_2 subjects. Then a simple way to test H0: rho_1 = rho_2 is to convert r_1 and r_2 via Fisher's variance stabilizing transformation ( z = 1/2 *

[R] error in using R2WinBUGS on Ubuntu 6.10 Linux

I am trying to run WinBUGS 1.4 from the Ubuntu 6.10 Linux distribution. I am using the R2WinBUGS packages with the source file listed below. WinBUGS appears to run properly, but I get the following message after WinBUGS starts in WINE. Does anyone know what may be causing this error and what

[R] significance test for difference of two correlations

Dear R users, how can I test, whether two correlations differ significantly. (I want to prove, that variables are correlated differently, depending on the group a person is in.) Greetings from Freiburg im Breisgau (Germany), Timo Stolz __

[R] lmer and scale parameters....

I'm using lmer to fit mixed-effect logistic regression models. This is for a small data set. First, I fit a constant: Generalized linear mixed model fit using Laplace Formula: propm ~ (1 | study) Data: inducedSR71507.dat Family: binomial(logit link) AIC BIC logLik deviance 183.7

Re: [R] Help with Dates

On 26 Jul 2007 09:59:31 -0400, Jeffrey J. Hallman [EMAIL PROTECTED] wrote: zoo is nice. 'tisFromCsv()' in the fame package is nicer. Jeff 1. What am I doing wrong here? I only get one data column. 2. I assume the regularized dates which do not exactly match the input ones are intended

Re: [R] substituting dots in the names of the columns (sub, gsub, regexpr)

Hi, A dot in a regular expression matches any character, so you have to escape each dot with backslash \\ (which itself is escaped in the string, to confuse things...). A plus symbol will match one or more of the preceding characters. A dollar symbol will match the end of a string. So:

[R] Average plan

Hello, I'm looking for a method to compute an average plan from 4 or 5 point in an cartesian space. I'm sure It can be done using a less-square method but maybe it a function already exist in R system to get this plan. Can somebody help me to solve this problem (I'm looking on the net for

Re: [R] Help with Dates

zoo is nice. 'tisFromCsv()' in the fame package is nicer. Jeff __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented,

[R] Odp: multiple graphs

Hi this particular graph is a combination of several approaches see layout # how to split plot window (or ?split) par(new=TRUE) # how to plot several times to the same window without erasing previous plot and of course sophisticated use of all other stuff which is available in R. See also

[R] substituting dots in the names of the columns (sub, gsub, regexpr)

Dear R users, I have the following two problems, related to the function sub, grep, regexpr and similia. The header of the file(s) I have to import is like this. c(y (m), BD (g/cm3), PR (Mpa), Ks (m/s), SP g./g., P (m3/m3), theta1 (g/g), theta2 (g/g), AWC (g/g)) To get rid of spaces and

Re: [R] logistic regression

Mary, The 10-group approach results in a low-resolution and fairly arbitrary calibration curve. Also, it is the basis of the original Hosmer-Lemeshow goodness of fit statistic which has been superceded by the Hosmer et al single degree of freedom GOF test that does not require any binning.

[R] ROC curve in R

Hi, I need to build ROC curve in R, can you please provide data steps / code or guide me through it. Thanks and Regards Rithesh M Mohan [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list

Re: [R] Convert string to list?

Is this what your want? as.vector(unlist(strsplit(str,,)),mode=list) Ross Darnell -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Manuel Morales Sent: Friday, 27 July 2007 10:39 AM To: r-help Subject: [R] Convert string to list? Let's say I have the

[R] Creating windows binary R package (PowerArchiver vs. zip -r9X)

Hi list,I apologize if you see funny fonts, b/c I'm using the new Windows Live Hotmail and don't know how to turn off the rich text mode.I have successfully built and installed a R package in windowsXP for R-2.5.1. But when I tried to create a .zip file so I can use Packages/install

[R] princomp error

I am attempting to run principal components analysis on a dataset of spectral reflectance (6 decimal places). I imported the data using read.table and there are both column and row headers. When I run princomp I receive the following error: Error in cov.wt(z) : 'x' must contain finite values

Re: [R] zeroinfl() or zicounts() error

On Thu, 26 Jul 2007, Rachel Davidson wrote: I'm trying to fit a zero-inflated poisson model using zeroinfl() from the pscl library. It works fine for most models I try, but when I include either of 2 covariates, I get an error. When I include PopulationDensity, I get this error: Error in

Re: [R] Large dataset + randomForest

Florian, The first thing that you should change is how you call randomForest. Instead of specifying the model via a formula, use the randomForest(x, y) interface. When a formula is used, there is a terms object created so that a model matrix can be created for these and future observations. That

Re: [R] ROC curve in R

On Thursday 26 July 2007 06:01, Frank E Harrell Jr wrote: Note that even though the ROC curve as a whole is an interesting 'statistic' (its area is a linear translation of the Wilcoxon-Mann-Whitney-Somers-Goodman-Kruskal rank correlation statistics), each individual point on it is an improper

Re: [R] significance test for difference of two correlations

There is R code for both the Fisher transform and the corresponding bootstrap procedure in the vignette for the proto package: http://cran.r-project.org/doc/vignettes/proto/proto.pdf On 7/26/07, Viechtbauer Wolfgang (STAT) [EMAIL PROTECTED] wrote: Let r_1 be the correlation between the two

Re: [R] error in using R2WinBUGS on Ubuntu 6.10 Linux

[EMAIL PROTECTED] wrote: I am trying to run WinBUGS 1.4 from the Ubuntu 6.10 Linux distribution. I am using the R2WinBUGS packages with the source file listed below. WinBUGS appears to run properly, but I get the following message after WinBUGS starts in WINE. Does anyone know what may

Re: [R] aggregate.ts

Jeff, I'm really not a fan of subjective mine is bigger than yours discussions. Just three comments that I try to keep as objective as possible. Bottom line: use 'tis' series from the fame package, or 'zoo` stuff from Gabor's zoo package. The last time I checked

[R] Problem installing tseries package

Hi, I'm running R 2.4.1 on Fedora Core 6 and am unable to install the tseries package. I've resolved a few problems getting to this point, by running a yum update, installing the gcc-gfortran dependency, but now I'm stuck. Could someone please point me in the right direction? R

Re: [R] dispersion_parameter_GLMM's

I agree with David. A dispersion parameter of 25 suggests that you have mainly 0's in your data set and your model is not adequate. Perhabs you should dichotomize your data in 0 and 1's and use a logistic mixed model but be aware of small numbers of events. That amount of overdispersion would

Re: [R] aggregate.ts

Your troubles with 'aggregate' for a ts are one of the reasons I created the 'tis' and 'ti' classes in the fame package. If you do this: x1 - tis(1:24, start = c(2000, 10), freq = 12) x2 - tis(1:24, start = c(2000, 11), freq = 12) y1 - aggregate(x1, nfreq = 4) y2 - aggregate(x2, nfreq = 4)

Re: [R] logistic regression

Maybe try making sure the data is numeric: fac.to.num=function(x) as.numeric(as.character(x)) On 26-Jul-07, at 9:34 AM, Sullivan, Mary M wrote: Greetings, I am working on a logistic regression model in R and I am struggling with the code, as it is a relatively new program for me. In

Re: [R] Obtaining summary of frequencies of value occurrences for a variable in a multivariate dataset.

Thanks so much Jim, Andaikalavan, Gabor and others for the help and suggestions. The solution will result in a matrix containing nested matrices to enable each variable name, each variables distinct value and the count of the distinct value to be accessible individually. The main matrix will

[R] colored heights in 3D plot (persp)

Hello everybody, I have a matrix with measurement values and plot them with persp. I want to highlight different heights in different colors. At least everything above and under a certain z-level shall have a different color to make the differences in height more obvious. How can I do that or

Re: [R] Creating a cross table out of a large dataset

On Thu, 2007-07-26 at 13:32 -0700, celine wrote: Dear all, I want to make a cross table out of a data set which is 2 columns wide and more than 15 rows long. When I use the table() function I get an error message This is the code I have used: Dataset - read.table(test.txt,

[R] Diagonal Submatrices Extraction

Yes you are right ... an example is mandatory. So ... I have a matrix of 0 with just a single 1 per row and per column I need to extract all maximal 'diagonal' submatrices Let's say I have the following matrix A B C D E a 0 1 0 0 0 b 1 0 0 0 0 c 0 0 1 0 0 d 0 0 0 1 0 e 0 0 0 0 1 well I would

Re: [R] Problem installing tseries package

On Thu, 26 Jul 2007, Michael Cassin wrote: Hi, I'm running R 2.4.1 on Fedora Core 6 and am unable to install the tseries package. I've resolved a few problems getting to this point, by running a yum update, installing the gcc-gfortran dependency, but now I'm stuck. Could someone please

Re: [R] Constructing bar charts with standard error bars

On 7/25/07, Ben Bolker [EMAIL PROTECTED] wrote: John Zabroski johnzabroski at gmail.com writes: The best clue I have so far is Rtips #5.9: http://pj.freefaculty.org/R/Rtips.html#5.9 which is what I based my present solution off of. However, I do not understand how this works. It seems

Re: [R] ROC curve in R

Note that even though the ROC curve as a whole is an interesting 'statistic' (its area is a linear translation of the Wilcoxon-Mann-Whitney-Somers-Goodman-Kruskal rank correlation statistics), each individual point on it is an improper scoring rule, i.e., a rule that is optimized by fitting an

[R] R codes for g-and-h distribution

hi! I would like to ask help how to generate numbers from g-and-h distribution. This distribution is like normal distribution but span more of the kurtosis and skewness plane. Has R any package on how to generate them? Any help will be greatly appreciated. Thank you so much! Form,

Re: [R] using contrasts on matrix regressions (using gmodels, perhaps): 2 Solutions

Dear list, I got two responses to my post. One was from Soren with a follow-up on personal e-mail, and the other I leave anonymous since he contacted me on personal e-mail. Anyway, here we go: The first (Soren): library(doBy) Y - as.data.frame(Y) lapply(Y,function(y){reg- lm(y~X);

Re: [R] ROC curve in R

Dylan Beaudette wrote: On Thursday 26 July 2007 06:01, Frank E Harrell Jr wrote: Note that even though the ROC curve as a whole is an interesting 'statistic' (its area is a linear translation of the Wilcoxon-Mann-Whitney-Somers-Goodman-Kruskal rank correlation statistics), each individual

Re: [R] dates() is a great date function in R

Mr Natural [EMAIL PROTECTED] writes: Just save the spreadsheet as a csv file and use tisFromCsv() in the fame package. One of the arguments tisFromCsv() takes is a dateFormat, so you can tell it what format the date column is in. You can also tell it the name of the date column if it isn't some

Re: [R] ROC curve in R

http://search.r-project.org/cgi-bin/namazu.cgi?query=ROCmax=20result=normalsort=scoreidxname=Rhelp02aidxname=functionsidxname=docs there is a lot of help try help.search(ROC curve) gave Help files with alias or concept or title matching 'ROC curve' using fuzzy matching: granulo(ade4)

Re: [R] Convert string to list?

Try this. It pastes list( onto the front and ) onto the end giving list( P = 0.0, T = 0.0, Q = 0.0 ) and then parses and evaluates that as an R expression. Str - P = 0.0, T = 0.0, Q = 0.0 eval(parse(text = paste(list(, Str, On 7/26/07, Manuel Morales [EMAIL PROTECTED] wrote: Let's say I

[R] reading stata files: preserving values of variables converted to factors

Hi, I am a Stata user new to R. I am using read.dta to read a Stata file that has variables with value labels. read.dta converts them to factors, but seems to recode them with values from 1 to number of factor levels (looking at the output of unclass(varname)), so the original numerical