similar to: help with rowsum/aggregate type functions

Dear Experienced R users, I have a looks-like simple but complicated problem urgently needed to be solved. Below is the detail: I have two dataframes, df1, df2. df1 contains two column and many thousands rows: column 1 is a "gene_name", column 2 is "value". df2 contains only one column which is "gene_name" with couple hundred rows. I want to change "value"

HI, Dear R community, My original file has 1932 lines, but when I read into R, it changed to 1068 lines, how comes? cdu@nuuk:~/operon$ wc -l id_name_gh5.txt 1932 id_name_gh5.txt > gene_name<-read.table("/home/cdu/operon/id_name_gh5.txt", sep="\t", skip=0, header=F, fill=T) > dim(gene_name) [1] 1068 3 -- Sincerely, Changbin -- Changbin Du DOE Joint Genome

for the script, please kindly see the script below. At line 10 and line 13, my problems occurs. The first one is I try to retrieve the gene official name from a column of a table. The pattern of official name is something starting with gene_name. For detail problems, please see the according lines. Any suggestions are appreciated example of matching source (extract the Nnat, sometime it would

Hi, I have the following data file to be parsed and captured as a data frame: __DATA__ #GDS_ID GENE_NAME GENE_DESCRIPTION GENE_FUNCTION 1007_s_at | DDR1 | discoidin domain receptor tyrosine kinase 1 | protein-coding 1053_at | RFC2 | replication factor C (activator 1) 2, 40kDa | protein-coding 117_at | HSPA6 | heat shock 70kDa protein 6 (HSP70B') | protein-coding __END__ In particular it is

Hi everyone, I am new to R-project. I did search through the list for my problem but i can't find it. I am sorry if this question has been asked. I would like to perform a correlation analysis between a hiv data and gene expression. Basically, i have a file that contains: hiv_name, start_position, end_position, chromosome. I would like to see if these data has anything to do with the

Hi, r-community, This morning, I MET the following problem several times when I try to attach the data set. When I closed the current console and reopen the R console, the problem disappear. BUt with the time passed on, the problem occurs again. Can anyone help me with this? > attach(total) The following object(s) are masked from total ( position 3 ) : acid base cell_evalue

Hi, I'm running simulations that include a function that occasionally fails because of an unpredictable singularity in a matrix that it tries to invert. I'd like to have the function return 'NA' when that happens, so that the simulations can continue. I've tried things like: test <- function() { options(error=return(NA)) x <- solve(0) return(x) }

Dear list, I wanna select the significant variables relative to bird distribution, using stepwise method. However, the result is always the best-fit model. Please kindly suggest if it is possible to show the selection process. Thank you Elaine [[alternative HTML version deleted]]

I am getting an error message, which I do not know the source to. I have a matrix SAMPLES that has preexisting rownames that I would like to change. GENE_NAMES contains these rownames. > rownames(SAMPLES) = GENE_NAMES Error in "dimnames<-.data.frame"(`*tmp*`, value = list(list(V1 = c(3843, : invalid 'dimnames' given for data frame > dim(SAMPLES) [1] 12626

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, I often work from home, running R on my office computer and displaying interactive graphics on my home computer using X11. This was always more sluggish than sitting at my office computer, obviously, but recently the graphics transfer has become painfully slow -- so slow, that I now divert the images to a postscript file and display that file remotely (which takes a second or two). I

Dear members of the R help list, I want to do a hierarchical glm with binomial family but am unsure about how to write the syntax which involves nesting. I want to test whether the risk of being attacked by Herbivores for Meadowsweet plants is significantly dependent on the Distance to heterospecific source plants. Dependent variable = Herbivory (yes/no) Explanatory continuous variable =

I do have a bunch of genes ( nearly ~50000) from the whole genome, which read in genomic ranges A range(gene) can be seem as an observation has three columns chromosome, start and end, like that seqnames start end width strand gene1 chr1 1 5 5 + gene2 chr1 10 15 6 + gene3 chr1 12 17 6 + gene4 chr1 20 25 6 + gene5

I'm trying to install R under Ubuntu 7.10 (gutsy; Linux 2.6.22-15-generic x86_64). Following the instructions at http://cran.r-project.org/bin/linux/ubuntu/README, I installed r-base, r-base-core, and r-base-dev without any problems. When I open R, however, I get the message "Can't open /usr/lib64/R/etc/ldpaths". That file is linked to /etc/R/ldpaths, which doesn't exist

Hi, I have the following data frame: > print(mydatframe) __DATAFRAME__ V1 V2 V3 1 1007_s_at DDR1 discoidin domain receptor tyrosine kinase 1 2 1053_at RFC2 replication factor C (activator 1) 2, 40kDa 3 117_at HSPA6 heat shock 70kDa protein 6 (HSP70B') __END__ Is there a way to create a hash with V2 as Key and V3 as its value? - Gundala Viswanath Jakarta - Indonesia

Hey everyone, I am an R-newby... so sorry for bothering you with simple-to-solve questions;) I have the following issue: trying to add labels to my scatterplots (with geom_dl in ggplot2). Everything works fine, but after checking every resource I do not find a way to change the font size of my labels. I tried size, cex, fontsize at every position... but it always stays the same. ggplot()+

Hi r-users, I want to use the sn package but I got the following message: > install.packages(repos=NULL,pkgs="c:\\Tinn-R\\sn_0.4-12.zip") Warning: package 'sn' is in use and will not be installed updating HTML package descriptions I did tried to do it a few times but it gives the same message.  ________________________________ From:

The function 'regsubsets' appears to calculate a BIC value that is different from that returned by the function 'BIC'. The latter is explained in the documentation, but I can't find an expression for the statistic returned by 'regsubsets'. Incidentally, both of these differ from the BIC that is given in Ramsey and Schafer's, The Statistical Sleuth. I assume