similar to: How to cite the the PDF user's guide for LIMMA

Dear R-Help, I am using the function "topTable" from the LIMMA package. To estimate adjusted P-values there are several options (adjust="fdr" , adjust="BH") as shown below: topTable(fit, number = 10, adjust = "BH", fit$Name) I guess any of these options (fdr, BH, etc.) is using a default of FDR=0.05 which is quite conservative (i.e., very

Dear R Users, In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best: bgcorrect.metod = rma rma2 mas normalize.method = qspline quantiles loess pmcorrect.method = pmonly subtractmm mas summary.method = liwong avgdiff medianpolish mas There are many options within each method. I would appreciate a hint on the best

Hi Martin, In using the Cluster Package, I have results for PAM and DIANA clustering algorithms (below "part" and "hier" objects): part <- pam(trout, bestk) # PAM results hier <- diana(trout) # DIANA results GeneNames <- show(RG$genes) # Gene Names are in this object But

Dear R users, I am using the beadarray package. I am trying to upload raw bead-level data using these commands: ######################################################## library(beadarray) datadir <- ("C:/Computer_programs/R/beadarray/cecilia") targets = read.table("targets.txt", sep = "\t", header = TRUE, as.is = TRUE) BLData = readIllumina(arrayNames =NULL,

In using the NLME package (R 2.6.1 for Windows), I am having a problem in running an R script that used to run with no problems using a Linux OS in 2004. So I am wondering if during these last ~3 yrs we had major changes in the syntax of the NLME package that I am not aware. This is the R script: library(nlme) treat=as.factor(c(1,2,1,2,1,2,1,2)) mouse=as.factor(c(1,1,2,2,3,3,4,4))

Dear R-Help, I am using the LIMMA User's Guide 5 January 2007 PDF version. For the example show in Section 7.4 DIRECT TWO-COLOR DESIGNS (pgs. 33-34), I could not grasp the rationale in developing the contrast.matrix with these R statements (">" indicates the R command prompt): > contrast.matrix <-

Hi Folks! I have a question regarding an issue on which I´ve read a few threads but can´t resolve --> Labelling every other tick mark on the x-axis using factors. Here´s an example: db<-data.frame(date=as.factor(c(1:50)),var=rnorm(50)) barplot(db$var,names.arg=levels(db$date),las=2,cex.axis=0.8,cex=0.8) This labels all the tickmarks in my barplot, which is the default behavior. I would

"Vallejo, Roger" <Roger.Vallejo at ARS.USDA.GOV> asked: > I would like to know if we can estimate Rg between two binary traits > (disease status: alive vs. dead) with the R package. > > My data: we have 100 full-sib (FS) families, > and two random samples (each with n= 200 FS fish) from each FS family > were evaluated for disease resistance to two different

I was trying to use memory.size() to determine whether a code loop I am executing created a memory leak, since one replicate of the simulation takes 670.98 seconds according to proc.time(), while 5 replicates takes 170762 seconds. So I set it up as: memA <- memory.size() looping code... memB <- memory.size() memA returns as 9.3, and memB returns 11.3. I'm not familiar with

I was wondering if there is a way to get read in a single keystroke at a time in R as a string, akin to ncurses-style interfaces. I looked into readLines, readChar, etc. using stdin, but these all require the use of an end of line. Has anyone ever had need to do this or have any ideas on how to do this? Thanks, Jon PS I apologize if this double-sends, but I am having mail client issues.

Dear all, I am having a hard time attempting to do a multinomial logit modeling in R. I am trying to analyze a dataset whereby there are 3 scenarios with 4 difference choice parameters. In particular ? I am having a hard time arranging this into a .csv format. What sorts of headings should I put in the column headers to reflect the variables and parameters for the total number of choice made

Hello I am using a Snom 190 and the quality seems OK. Trouble is the volume is quite low and full volume on the Snom is still too low. Is there something I can do on the asterisk to increase the volume? Angus

Hello, I am trying to compile the R package on a sun. I get the error message rbitmap.c: In function 'my_png_error': rbitmap.c:73: structure has no member named 'jmpbuf' rbitmap.c: In function 'R_SaveAsPng': rbitmap.c:122: structure has no member named 'jmpbuf' make[4]:*** [rbitmap.lo] Error 1 Has anyone encountered this problem? Any solutions? Is there are

Hi, I am trying to read in my Affymetrix CEL files (48 files, total ~600 MB) but I keep getting memory errors. Can somebody please help me with this. Or is therea remote server I can send my data to for computation? Any help is much appreciated. Thanks Dr. Tristan Coram Postdoctoral Research Associate Research Plant Pathologist/Geneticist United States Department of

I have a need to find the order of number to get a scaling parameter as a power of 10. I have a function that works *so far*, but it is ugly and probably buggy. In the interest of avoiding code-based outliers in my data, I thought I would ask if anyone here has a better way. > scl <- function(x){ + length(charToRaw(format(trunc(x), scientific = F)))-1} > a <- 123456789 > b <-

All- Does anyone on the list have experience with building RODBC from source on a Linux box for use with DB2? I am using (all from source): R 2.0.1 unixODBC 2.2.9 RODBC 1.1-3 For example: [jcole]$ R CMD INSTALL RODBC_1.1-3.tar.gz 2> rodbc.log * Installing *source* package 'RODBC' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether

Buenas tardes a tod@s, Estoy incursionando en el analisis de tweets utilizando el paquete twitteR y siguiendo http://www.webmining.cl/2012/07/text-mining-de-twitter-usando-r/ Desafortunadamente cuando ejecuto # cargar librerias library(twitteR) library(tm) library(wordcloud) # recolecta tweets de @camila_vallejo tweets = userTimeline("camila_vallejo", 2000) obtengo Error in

Como integrar asterisk con Ldap.?? Saludos -- Dario Javier Estupi?an Vallejo darioestupinan at soygenial.co Investigaci?n y Desarrollo - Neiva Corporaci?n Polit?cnica Nacional ................................................. -------------- next part -------------- An HTML attachment was scrubbed... URL:

Saludos, necesito saber la ubicaci?n del archivo con contrase?as por default para porder ocultarlo. Gracias. I need to know the addres or location of file with passwords for default thanks! -- Dario Javier Estupi?an Vallejo darioestupinan at soygenial.co Investigaci?n y Desarrollo - Neiva Corporaci?n Polit?cnica Nacional ................................................. -------------- next

Saludos, Como oculto una carpeta en asterisk sin da?ar la informaci?n ejemplo: cdr_mysql.conf gracias -- Dario Javier Estupi?an Vallejo darioestupinan at soygenial.co Investigaci?n y Desarrollo - Neiva Corporaci?n Polit?cnica Nacional ................................................. -------------- next part -------------- An HTML attachment was scrubbed... URL: