search for: eleni

Hi all! I am new to R and I would like to ask you the following question:How can I substitute the NA values with 0 in a data frame? I cannot find a command to check if a value is NA... Thank you very much! Eleni

...to install the package "GEOquery" in unix. I have downloaded the standard version of R and this package is not contained in the default. I know that I can select repositories under windows but I don't know how to do it in unix. Does anyone have any idea on this? Thank you in advance, Eleni [[alternative HTML version deleted]]

...use it. Are you aware of any reputable places (academic or not) that use R? (e.g. maybe you work for them) I would be really grateful for any advice on this. Also suggestions on arguments I could use to persuade them that R is so much better than Excel would be very much appreciated. Many Thanks Eleni Rapsomaniki

...r curve and I found online that Kaplan - Meier estimates are computed with a function called km in the event package. Is there an update for that because when I choose to download packages in R,. there is no package called event, even though I have selected all the repositories. Thanks in advance, Eleni [[alternative HTML version deleted]]

...I reject the null hypothesis and I accept the alternative one, that I have greater gene expression in positive than in negative. I assume I must be doing sth wrong because the heatmap that I get with the genes that pass the filter of p-value is wrong. Could anyone help me with this? thanks a lot, Eleni [[alternative HTML version deleted]]

...ose for example method="complete", how are the distances between the elements calculated? Are they taken form the dissimilarity matrix I have provided as the first argument? clust.complete.agnes<-agnes(as.dist(D),diss="TRUE",method="complete") Thank you very much, Eleni [[alternative HTML version deleted]]

...any other similarly super-efficient function)? example: #Suppose a matrix: m1=cbind(1:5,1:5,1:5) #The aim is to create a new matrix with every column containing the cumulative sum of all previous columns. m2=m1 for(i in 2:ncol(m1)){ m2[,i]=apply(m1[,1:i],1,sum) } m2 Many thanks in advance Eleni Rapsomaniki Research Associate Strangeways Research Laboratory Department of Public Health and Primary Care University of Cambridge ?

...he office PC and kept it in a usb drive. When I tried to open it on my laptop I got an error: "Fatal Error: Unable to restore saved data in .RData". On both computers I have the R.2.9.0 version. Could anybody give me an explanation why this happens and how I can solve this? Thanks a lot! Eleni [[alternative HTML version deleted]]

...norm(20,4.2,1.1) plot(density(r2), col="blue") lines(density(r1), col="red") Is there a way in R to compute/estimate the point(s) x where the density of the two distributions cross (ie where x has equal probability of belonging to either of the two distributions)? Many Thanks Eleni Rapsomaniki PhD student Birkbeck College, UK

...ng risks, adjusted for the individual's covariates? The only thing that seems to come close is the cuminc function from cmprsk package, but I would like to adjust for more than one covariate (it allows you to stratify by a single grouping vector). Any help/tips will be extremely appreciated. Eleni Rapsomaniki Research Associate Cambridge [[alternative HTML version deleted]]

...age I can plot it the polynomials and fitted coefficients as: plot(0.407*I((age/100)^-2) + -4.96*I((age/100)^-0.5) ~ age, GBSG) But I can't work out how to get a 95% confidence interval for this curve... Any suggestions? I could bootstrap it, but is there a mathematical solution? Many thanks Eleni Rapsomaniki Medical Statistician UCL, London

...rror: "Cannot allocate vector of 2.4 Mb". I increase the memory.limit to 4000 (which is the largest supported by my computer) but I still retrieve the error because of other big variables that I have in the workspace. Does anyone know how to overcome this problem? Many thanks in advance, Eleni [[alternative HTML version deleted]]

You need to give us more details, like how you call randomForest, versions of the package and R itself, etc. Also, see if this helps you: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/32918.html Andy From: Eleni Rapsomaniki > > Dear all, > > I am trying to train a randomForest using all my control data > (12,000 cases, ~ 20 explanatory variables, 2 classes). > Because of memory constraints, I have split my data into 7 > subsets and trained a randomForest for each, hoping that &gt...

Dear R users, I know one way to see the code for a hidden function, say function_x, is using default.function_x (e.g. summary.default). But how can I see the code for imported packages that have no namespace (in this case Design)? Many Thanks Eleni

...der the cutoff found by "performance" but to use another cutoff that I calculate. How could I change the following command in order to get what I want? perform=performance(pred,measure="auc",x.measure="cutoff"), where pred is a prediction object. Thank you very much, Eleni [[alternative HTML version deleted]]

Hello all, I have the following problem. I want to insert blank rows in an data frame so as to make it comparable with another data frame with more rows. How can I insert these rows? If this is not solvable, then, alternatively, is it easy to delete rows from a data frame? Thanks for helping, Eleni [[alternative HTML version deleted]]

...ctions). The following: updated.forml=update(forml, ~ . -A) #gives me this: #Surv(time, status) ~ x1 + x2 + x3 + x4 + B + x5 + strata(sex) + A:x3 + A:x4 + B:x5 #but I want this: #updated.forml=as.formula("Surv(time, status) ~ x1+x2+x3+x4+B*x5+strata(sex)") Any ideas? Thanks in advance Eleni Rapsomaniki Research Associate Strangeways Research Laboratory Department of Public Health and Primary Care University of Cambridge ?

...ng raw Affymetrix CEL files and I am using the Michigan custom CDF library hgu133plus2hsentrezgprobe. I have been looking for documentation on the function that it contains...I am specifically interested in converting probe names to gene symbols. Does anybody know where I can find it? Thank a lot! Eleni [[alternative HTML version deleted]]

...'t think of an intelligent way to make them work! The second problem is that I also need to know how many degrees of freedom (ie non missing pairs of values) were used in each correlation. Is there a way to also do this efficiently? I hope this makes sense! Thank you all very much in advance! Eleni

...ected vs observed probabilities). Any other functions I should be aware of? Also, has anybody come across an implementation of the statistic described in: "A global goodness of fit statistic for Cox regression models" by Parzen & Lpisitz, Biometrics 55, 1999 Many thanks in advance Eleni Rapsomaniki Research Associate Strangeways Research Laboratory Department of Public Health and Primary Care University of Cambridge ?