similar to: how to calculate mean into a list

Dear listers, a little off-topic: I am looking for and compare algorithms which can calculate "distance" or "similarity" between two gene lists with different lengths. Any paper, any implementation in R and any suggestion is welcome! Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..."

Dear Listers: For example, if I have a .R source file which has more than one function, and I want to just load only one of the functions, how could I do that? (removing the rest after sourcing is not what I intend b/c in my workspace, I might have some of the rest and I don't want to change my workspace: i.e., I only change my workspace by adding one function from a R source file). Thanks,

Hi, I searched the archives and did not find a good solution to that. assume I have 10 sets and I want to have the common character elements of them. how could i do that? -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Hi, there: I am wondering if there is a quick way to "reverse" a list like this: t0 <- list(a=1, b=1, c=2, d=1) reverst t0 to t1 > t1 $`1` [1] "a" "b" "d" $`2` [1] "c" thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Hi, I am wondering how to make a function Fun to make the following work: t0 <- (paste("hgu133a", "ENTREZID", sep="")) xx <- as.list(Fun(t0)) # make it work like xx<-as.list(hgu133aENTREZID) thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Dear Listers: I have a couple of data frames to report and each corresponds to different condtions, e.g. conditions=c(10, 15, 20, 25). In this examples, four data frames need to be exported in a "pretty" report. I knew Perl has some module for exporting data to Excel and after googling, I found R does not. So I am wondering if there is a package in R for generating good reports. I

hi, is there some good summary on clustering methods in R? It seems there are many packages involving it. And I have two questions on clustering here: 1. Is there a way of evaluate the effecitives (or seperation) of clustering (rather than by visualization)? 2. Is there a search method (like genetic search) which can help find the best subset of attributes which gives best seperation? Thanks,

hi, if I have 20 x 3 data.frame, how to split it into 10 x 6 (moving the lower part of 10x3 to column) or 5 x 12 thanks -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Dear Listers: I have a question on loading objects from workspace: suppose I have two workspaces for two approaches. My old workspace has some objects I need for the new workspace but I don't want to load the whole old workspace and remove most of the old objects and get what I want. Is there an easier way to do like this: load "some needed obj" from old workspace, which has been

Hi, there: Assume I have a dataframe with rownames like A with rownames like a to e, > A [,1] [,2] a 1 6 b 2 7 c 3 8 d 4 9 e 5 10 when I use A[1,], I lost the rowname for it, like below. How could I keep it? Is there an easy way instead that I have to modify by myself after I used A[1,] manually. > A[1,] [1] 1 6 Thanks, W. -- Weiwei Shi, Ph.D Research

Hi, there: Suppose I have a couple of data.frames and each one has five columns (one for x-axis, two for y-axis and two for std of y's.) There is another dimensions (besides x and y) which is continuous. My question is, how to plot such series of data frames in one plot (thus, 3-dimensional plot) AND multiple 2-D plots. I am not familar with R's plotting utilities. Thanks. -- Weiwei

hi, i have a data frame like this: 0.3 0.7 0.4 0.8 i am trying to plot this data frame and each cell is filled with different colors based on the value. Is there a function which can do this? thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Hi, I am using dlda algorithm from supclust package and I am wondering if the output can be a continuous probability instead of discrete class label (zero or one) since it puts some restriction on convariance matrix, compared with lda, while the latter can. thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..."

Dear all, I have a question on Cohen's kappa: Assume I have two datasets, one has 500 objects, 10 methods and the other, 1000 different objects, 20 different methods. Could I compare between the two datasets to conclude the 10 methods are more "concordant" than the 20 ones by looking at some output, for example, cohen.kappa{concord} ? One more, could anyone explain in brief,

hi, I have a conversion table for colnames like this: Probe_ID HUMAN_LLID 1 AF106325_PROBE1 7052 2 NM_019386_PROBE1 7052 3 NM_012907_PROBE1 339 4 AW917796_PROBE1 84196 5 L27651_PROBE1 10864 The Probe_ID contains a list of colnames for another data.frame, say x1. I need to convert such colnames to another ID's system, HUMAN_LLID by using the table.

Hi, I am wondering how I can write a help page for my own function so when I type ?myOwnfunc, then the help page will show up? thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Hi, anyone interested in this: I tried to simply this loop with lapply or something but haven't figured it out: mapt = c("203929_s_at", "203930_s_at", "203928_x_at", "206401_s_at") mapt.combn <- lapply(1:4, function(i) combn(mapt, i)) out = list() k = 1 for (i in 1:length(mapt.combn)){ for (j in 1:ncol(mapt.combn[[i]])){ out[[k]] =

Dear Listers: I used cronbach{psy} to evaluate the internal consistency and some set of variables gave me alpha=-1.1003, while other, alpha=-0.2; alpha=0.89; and so on. I am interested in knowing how to interpret 1. negative value 2. negative value less than -1. I also want to re-mention my previous question about how to evaluate the consistency of a set of variables and about the total

Hi, I am trying to print out my confusion matrix after having created my random forest. I have put in this command: fit<-randomForest(MMS_ENABLED_HANDSET~.,data=dat,ntree=500,mtry=14, na.action=na.omit,confusion=TRUE) but I can't get it to give me the confusion matrix, anyone know how this works? Thansk! Ruben [[alternative HTML version deleted]]

Hi, I am writing a generic function and need to check if an arg is a data frame or not. I could use is.null(dim(x)) to get what i want. But i want to know if there is a function which can tell me whether it is a list, a numeric vector, a data frame, a factor and so on. Can R do that? thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did