search for: genego

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

...sters, 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..." ---Matrix III [[alternative HTML version deleted]]

...ring 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, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

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

...s 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, what's the difference between kappa(Cohen) and kappa(Siegel)? Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]]

...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..." ---Matrix III

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

...ow 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, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

...d 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 Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

...after googling, I found R does not. So I am wondering if there is a package in R for generating good reports. I found package xtable but it seems (if not, please correct me) that it can only generate one table for one file. Thanks for any suggestions, -W -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

...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 correlation (my 2 cent to answer the question). Is there any function in R to do that? Thank you very much! -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

...r ID's system, HUMAN_LLID by using the table. The colnames of x1 with the same names (in HUMAN_LLID) need to be averaged. Is there a good way to do it? I also put this question in bioconductor since I believe it might be solved by some package. thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

...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 not. But I believed..." ---Matrix III

...l(mapt.combn[[i]])){ out[[k]] = mapt.combn[[i]][,j] k = k + 1 } } out # the following two lines create a list of list, which is not my intended: y0 = mapt.combn lapply(1:4, function(j) {n=ncol(y0[[j]]); lapply(1:n, function(i) y0[[j]][,i])}) 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 this task and suppose a0 is a list of 10 data.frames, I want to calculate like this > (a0[[1]]+a0[[2]]+..+a[[10]])/10 Thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

...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 Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]]

...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 implemented in R? 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 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