similar to: Appending 4 Digits On A File Name

Greetings all, I am getting an error message that is stifling me. Any ideas? > ## Define Directories ## > load_from <- "/home/mcc/Dropbox/abrodsky/kegg_combine_data/" > save_to <- "/home/mcc/Dropbox/abrodsky/ttest_results/" > > ############################### > ## Define Columns To Compare ## > compareA <- "log_b_rich" > compareB

Greetings all, I am getting this error that is driving me nuts... (not a long trip, haha) I have a set of files and in these files I want to calculate ttests on rows 'compareA' and 'compareB' (these will change over time there I want a variable here). Also these files are in many different directories so I want a way filter out the junk... Anyway I don't believe that this is

Greetings all, I am calculating two t-test values for each of many files then save it to file calculate another set and append, repeat. But I can't figure out how to write it to file and then append subsequent t-tests. (maybe too tired ;} ) I have tried to use "dump" and "file.append" to no avial. ttest_results = tempfile() two_sample_ttest <- t.test (tempA, tempB,

Greetings all, I have been working with RStudio and R only for a little while. I came across a package called 'reshape' that helped me 'rename' columns. Unfortunately, my computer got hosed (too much playing with linux too late at nite) and I had to re-install everything, BUT when I tried to reinstall 'reshape' or 'reshape2' I COULDN't. Is there a way to get

Hi all, I have a list that I got from a web page that I would like to crunch. Unfortunately, the list has some unusual separators in it. I believe the columns are separated by 1 space and 1 tab. I tried to insert this into the read.table( ..., sep=" \t", ...) but got an error that said something like 'only one byte separators can be used. I have thought about using a gsub to

Greetings all, I am curious to know if either of these two sets of code is more efficient? Example1: ## t-test ## colA <- temp [ , j ] colB <- temp [ , k ] ttr <- t.test ( colA, colB, var.equal=TRUE) tt_pvalue [ i ] <- ttr$p.value or Example2: tt_pvalue [ i ] <- t.test ( temp[ , j ], temp[ , k ], var.equal=TRUE) ------------- I have three loops, i, j, k. One to test the all of

i don't know perl,but on server site,they give soap:lite using perl , go to--->http://www.kegg.jp/kegg/soap/doc/keggapi_manual.html i want to download data from kegg server ,using R only, how to proceed? & what is mean by SOAP client driver ? also go to http://soap.genome.jp/KEGG.wsdl -- View this message in context:

My conception of how NAMESPACE and methods in R-2.7.0 resolved a generic 'func' to a func-method was to search as follows: In 2.7.0: func --> NAMESPACE, including Imports: (and other details) --> .GlobalEnv, and eventually Depends: since these are on search() In R-devel it seems like func --> NAMESPACE, including Imports: (and other details) --> ?? but not

As far as I know, the following should work. Can anybody tell me if/where I am going wrong? > packageDescription("KEGG", field="Version") [1] "1.6.4" > require(KEGG, version="1.6.4") Loading required package: KEGG [1] FALSE Warning message: There is no package called 'KEGG', version 1.6.4 in: library(package, character.only = TRUE, logical

Hi all , I am facing some problems with 'ls' command. Whenever I use it I get the following error : ls("KEGG.db") Error in as.environment(pos) : no item called "KEGG.db" on the search list ls("pkgname") Error in as.environment(pos) : no item called "KEGG.db" on the search list and this is true for any package. Can anything be done

Hi All, I am learning R and having a little trouble with the usage and proper definitions of data.frames vs. matrix vs vectors. I have read many R tutorials, and looked over ump-teen 'cheat' sheets and have found that no one has articulated a really good definition of the differences between 'data.frames', 'matrix', and 'arrays' and even 'factors'. I

Hi, I'm using GAGE/pathview to analyze my RNA-seq and phospho-protein data. The following error occurs after this command line below: >pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview( gene.data = cnts.d, pathway.id = pid, gene.idtype="SYMBOL",kegg.native = F, same.layer = T, species = "hsa", kegg.dir = "test", out.suffix = "up"))

Hi guys, Having a weird issue with a Dom0. When we were running 2.6.18.8 kernel the server would lock up every 2 weeks for no reason. Its been a difficult one to resolve as there are no errors. We have now upgraded to 2.6.32.13 and the lock ups are more often. For example today it crashed in the morning, then it was rebooted and it crashed again about 5 hours later, no logs. The

Hi all I am not a C programmer, but I am trying to understand formatC to get consistent printing of reals to a given number of significant digits. Can someone please explain this to me? These first three give what I expect on reading ?formatC: > formatC(0.0059999, digits=2,format="fg",flag="#") [1] "0.0060" > formatC(0.59999,

Hi all After posting what follows, Duncan Murdoch suggested perhaps a bug in formatC, or an error on documentation. Any comments? In particular, bug, error or not, any ideas about how I can consistently get two significant figures to print? P. ---------- Original Message ---------- Hi all I am not a C programmer, but I am trying to understand formatC to get consistent printing of

Greetings! OS: Windows R 2.0.1 Before anyone flames -- I tried to query this on the R searchable web site and using google and did not find anything applicable. As of about a week ago the help.search function dies when used in the simple help.search("something") usage. The error is Error in rbind(...) : number of columns of matrices must match (see arg 203) After some effort I have

Is this a bug somewhere? The format function, using a specific number of digits, doesn't give sensible results: R> set.seed(2);print(x<-rexp(5)) [1] 1.86535 0.40475 0.14665 1.73071 0.08953 R> format(x,digits=1) [1] "1.87" "0.40" "0.15" "1.73" "0.09" R> format(x,digits=2) [1] "1.87" "0.40" "0.15"

This, for example: v <- c(9.6996, 99.99) formatC(v, digits=3, format="g") shows: " 9.7" " 100" This is scientifically incorrect for the first number in the sense that I like to show all 3 significant digits, including trailing zero's. Is there a way that the first number would show as " 9.70"? By the way, can't use format() since it applies

Hi there, i'm not getting along with the following problem. I'd like to print a real number, e.g. x <- 12.3 with exactly two digits after the decimal point, e.g. 12.30 I've tried the whole format(), formatC() and prettyNum() functions but did not have any success with it. This should work with all real numbers, in case even with 0.0 (-> 0.00). For cracks this thing is pretty

Dear All, I was trying to format a numeric vector (100*1) by using outd <- format(x=m, sci=F, digits=2) > outd[1:10] [1] " 0.01787758" "-0.14760306" "-0.45806041" "-0.67858525" "-0.64591748" [6] "-0.05918100" "-0.25632276" "-0.15980138" "-0.08359873" "-0.37866688" >m[1:10] [1]