similar to: Filling dataframe incorrectly in for loop

Hello list. I have a vector of values: eg > head(diff_mirs_list) [1] "hsa-miR-26b" "hsa-miR-26b" "hsa-miR-23a" "hsa-miR-27b" "hsa-miR-29a" [6] "hsa-miR-29b" and I would like to conditionally replace each value in this vector with a number defined in a dataframe: > fc ???????????? Probe ave.fc 1?????? hsa-let-7a?? 1.28 2?????

Hi, When I look at the summary of an rpart object run on my data, I get 7 nodes but when I plot the rpart object, I get only 3 nodes. Should the number of nodes not match in the results of the 2 functions (summary and plot) or it is not always the same? Look forward to your reply, Carol -------------------------------------------- ?summary(rpart.res) Call: rpart(formula = mydata$class ~ ., data

Hi, There is a question that I am confused. I have a set of data like this: hsa-miR-205--GATA3 0.797882767 1.08E-13 hsa-miR-205--ITGB4 0.750217593 1.85E-11 hsa-miR-187--PGF 0.797604155 3.24E-11 hsa-miR-205--SERPINB5 0.744124886 3.28E-11 hsa-miR-205--PBX1 0.734487224 7.89E-11 hsa-miR-205--MCC 0.72499934 1.80E-10 hsa-miR-205--WNT5B 0.717705259 3.33E-10 hsa-miR-200c--PKN2 0.721746815

Through converting a miRNAs file from FASTA to character format I get a vector which looks like the following: > nml [1] "hsa-let-7a MIMAT0000062 Homo sapiens let-7a" [2] "hsa-let-7b MIMAT0000063 Homo sapiens let-7b" [3] "hsa-let-7c MIMAT0000064 Homo sapiens let-7c" [4] "hsa-let-7d MIMAT0000065 Homo sapiens

Hello everyone, Im working with graphNEL object and want to extract all the nodes which have adjacent nodes with at least 20 nodes in between them. acc(graph, graphnodes) obviously provides a list for the accessable nodes of every node from a node and a number of the edges between them. Like this: $`hsa:8379` hsa:100131844 hsa:10393 hsa:246184 hsa:29882 hsa:29945 1

I have the following vector of strings (shown only the first 3 elements) > desc[1:3] [1] "hsa-let-7a MIMAT0000062 Homo sapiens let-7a" [2] "hsa-let-7a* MIMAT0004481 Homo sapiens let-7a*" [3] "hsa-let-7a-2* MIMAT0010195 Homo sapiens let-7a-2*" > is.vector(desc) [1] TRUE > A <- unlist(strsplit(desc[1:3], " ")) > A [1]

*I have the following function:* /plot_mi_time = function(mdata, miname) { mdata2 = mdata[row.names(hakat) == miname, ] print(mdata2) xcoords <- c(1,1,2,2,3,3,4,4,5,5,6,6) plot(c(xcoords), mdata2, xaxt="n", ylab="Expression", xlab="Time(h)", , main=miname) axis(1, at=xcoords,

Hello List I'm moving this over from the bioC list as, although the problem I'm working on is biological, the current bottle neck is my poor understanding of R. I wonder if someone would help me with the following function. cumulMetric <- function(deMirPresGenes, deMirs){ ??? #need to match position of each miR in deMirPresGenes with its FC to form a vector of FC in correct order ?

Hi, I have a question about heatmap. I have a data with row as microRNA and two columns are two cell expression values for these microRNA. So, like: cell1 cell2 miRNA1 1.5 3.4 miRNA2 1.3 2.4 ................... miRNA50 5 2.1 miRNA51 7.3 0.5 I want to see some miRNA are high in cell1 and low in cell2 but others are low in cell1 and high in cell2. I

Hi guys, one of the questions where you need a real human instead of a search engine, so it would be great if you could help. I have a matrix of z-scores which I would like to filter, sometimes columnwise, sometimes rowwise. Data looks like this: Allstar hsa.let.7a hsa.let.7a.1 hsa.let.7a.2 2 0.87 0.79 -0.57 1.07 3 0.67 -1.14 -0.78 -0.95 4

I have the following list of strings: name <- c("hsa-miR-555p","hsa-miR-519b-3p","hsa-let-7a") What I want to do is for each of the above strings replace the text after second delimiter with "zzz". Yielding: hsa-miR-zzz hsa-miR-zzz hsa-let-zzz What's the way to do it? [[alternative HTML version deleted]]

Hi Christian, Chuck (and lists) It seems that the problem may be the strange behaviour of 'unstack' inside a function. See this thread in the R mailing list: http://tolstoy.newcastle.edu.au/R/help/04/03/1160.html Anyway, I got round the problem by using 'aggregate' instead of converting to a list and then tapply to sum values of metric. Probably more efficient as well. Thanks

dear group, i have 100 files starting with 'hsa-*'. ex. file: fruit p-value ------------ apple 0.0003 orange 0.004 kiwi 0.0003 peach 0.0004 I want to read all these files and create a single matrix. here each file may have different fruit names. in the matrix i want to have a union of all fruits and those should be the rows in the matrix and file names should be columns.

Hi everyone, I am trying to find a way to filter a table; If I am given for example the following table: > head(intra) chr miRNA start end strand ACC hsa_ID region region_start region_end gene_id transcrip_id 1 chr1 miRNA 1102484 1102578 + ACC="MI0000342"; ID="hsa-mir-200b"; exon 1102484 1102578 NR_029639 NR_029639 2 chr1

Hello, please see below my code for a heatmap. Unfortunately my column names do not completely appear. Can you please send me the appropriate code to visualise them? Many Thanks! Nils library(GMD) dat<-data.frame(EntryA=as.numeric(c(4.24,3,1.66,1.28,1.2,-1.32,-1.88)), EntryB=as.numeric(c(4.16,4.82,-1.82,-3.02,0.99,1.1,-3.31)))

Hi, I have two questions want to ask. 1. If I have a matrix like this, and I want to figure out the rows whose value in the 3rd column are less than 0.05. How can I do it with R. hsa-let-7a--MBTD1 0.528239197 2.41E-05 hsa-let-7a--APOBEC1 0.507869409 5.51E-05 hsa-let-7a--PAPOLA 0.470451884 0.000221774 hsa-let-7a--NF2 0.469280186 0.000231065 hsa-let-7a--SLC17A5

Any ideas about the following problem: I have a matrix (A) that looks like this: gene_names values hsa-mir-124 0.3 hsa-mir-234 0.1 hsa-mir-344 0.4 hsa-mir-333 0.7 ..... ....... (This is a 2 by 22283 matrix: quite large) I would like to plot the values, but output the gene_names as the plotting symbol. I have tried

Hi Mr. Liu, Thanks for your quick reply. I compiled the code with the libclc_trunk and linked the bitcode file under $LIBCLC_DIR/built_libs/tahiti-amdgcn--.bc. After looking into the libclc, it is currently using the new workitem intrinsics (commit ba9858caa1e927a6fcc601e3466faa693835db5e). In the linked bitcode ($LIBCLC_DIR/built_libs/tahiti-amdgcn--.bc), it has the following code segment,

Dear Developers, I compiled a OpenCL kernel before (on Nov. last year) like __kernel void g(__global float* array) { array[get_global_id(0)] = 1; } with libclc, which would originally use the instrinsics like llvm.r600.read.local.size.x(). I executed the generated object file with one version of the hsa-runtime [1] provided by Mr. Stellard, when there was more than one workgroup, the output

Hi, Please Help! My normal users are able to gain access to all home directories even though the group owner is Domain Admins. I have set the permissions to 770 while testing and the group to Domain Admin on all directories. I have a Server2003 AD Domain with a clustered RHEL5 samba server for the home directory. I am using samba 3.0.23 with Winbind and LDAP idmap backend. This server is