similar to: Limitation to R Question

Thanks for all your great answers. The app I?m working on is indeed an exploratory data analysis tool for gene expression, which requires a bunch of bioconductor packages. I guess for now, my best solution is to divide my app into modules and load/unload packages as the user switch from one module to another. This brought me another question: it seems that unload package with the

Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view,

On 04/05/2016 08:44, Martin Maechler wrote: >>>>>> Qin Zhu <qinzhu at outlook.com> >>>>>> on Mon, 2 May 2016 16:19:44 -0400 writes: > > > Hi, > > I?m working on a Shiny app for statistical analysis. I ran into this "maximal number of DLLs reached" issue recently because my app requires importing many other packages.

Hi, I have two data set of normalized Affymetrix CEL files, wild type vs Control type.(each set have further three replicates). > wild.fish AffyBatch object size of arrays=712x712 features (10 kb) cdf=Zebrafish (15617 affyids) number of samples=3 number of genes=15617 annotation=zebrafish notes= > Dicer.fish AffyBatch object size of arrays=712x712 features (10 kb) cdf=Zebrafish (15617

Hi there, I got a problem when trying to read in a .cel file using ReadAffy(). R codes: require(affy) ReadAffy(filenames="CH1.CEL") It failed and I got the error, Error in read.celfile.header(as.character(filenames[[1]])) : Is CH1.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats Also, I tried

Hi, I am a Ph.D. student from Québec, Canada. I’m a beginner with R and Bioconductor. Until now the only experience I have is in analyzing microarray data using affy and limma packages. Now I am trying to analyze Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth moderated t test on those arrays. Since no cdf official package is available for those arrays, after reading many

Dear Help, After loading the pd.Citrus library and checking the DataFrame, I ran > the R code for: > > 1) 'oligo' > > > > {> library(pd.citrus) > Loading required package: RSQLite > Loading required package: DBI > > data(pmSequence) > > > show(pmSequence) > DataFrame with 341730 rows and 2 columns > fid sequence > <integer>

LLVM3.8 version. https://bugs.llvm.org//show_bug.cgi?id=24233. The example can catch exception. But I use my own code for testing, CustomEHMemoryManager allocated memory address is very large, allocateCodeSection, allocateDataSection assigned address (more than 32 bit address space) is getting smaller and smaller. Cause registerEHFrames to fail. 3.9.1 or 4.0.0 version has been supported on win

Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fact, that most genes have

Hi Scott, Thanks for the patch. I'm not really involved in R development; it will be up to someone in the R core team to apply it. I would hazard to say that even if correct (I haven't checked), it will not be applied because the change might break existing code. For example it seems like reasonable code might easily assume that a column with the same name as "by.x" exists in

Hi I am new in using R. I am facing problem getting the raw data like the mean value, standard deviation value form the .CEL file. Please help me, how can I get these raw information from a .CEL file into an exel file? Thanks -- View this message in context: http://r.789695.n4.nabble.com/raw-data-form-CEL-file-tp2245796p2245796.html Sent from the R help mailing list archive at Nabble.com.

dear all I got this error when I try to use libspeex in visual studio. when I include speex/speex_echo.h, it complains about unresolved external symbol _speex_echo_state_init. And when I include mdf.c into the source, it generates whole bunch of errors. Any idea? thanks so much --------------------Configuration: audio - Win32 Debug-------------------- Compiling... mdf.c C:\Documents and

Hi-- While I agree that we cannot agree on the ideal algorithms, we should be taking practical steps to implement microarrays in the clinic. I think we can all agree that our algorithms have some degree of efficacy over and above conventional diagnostic techniques. If patients are dying from lack of diagnostic accuracy, I think we have to work hard to use this technology to help them, if we

Hi, I was unable to find a bug report for this with a cursory search, but would like clarification if this is intended or unavoidable behaviour: ```{r} # Create example data.frames parents <- data.frame(name=c("Sarah", "Max", "Qin", "Lex"), sex=c("F", "M", "F", "M"),

Hi everyone, My purpose is to read a .CEL file into R. The .CEL file was created from a .CAB by using DTT software found on Affymetrix website I read the .CEL file in R using ReadAffy as follows: > d2=ReadAffy(widget=T) and I complete the fields as required. It does not complain. For example I could find the description: > description(d2) Experimenter name: BB Laboratory: FFL Contact

Thanks Duncan and Frederick, I suspected as much - there doesn't appear to be any reason why conflicts between by.x and names(y) shouldn't and cannot be checked, but I can see how this might be more trouble than its worth given it potentially may break downstream packages (i.e. any cases where this occurs but they expect the name of the key column(s) to remain the same). Best, Scott On

Hi Mats, I think Kevin's point is malloc can return 0, if malloc/free pair is optimized way, the semantic of the original would be changed. On the other hand, malloc/free are special functions, but programmers can still define their own versions by not linking std library, so we must assume malloc/free always have side-effect like other common functions, unless we know we will link std

Sir, Kindlly Guide me how to get the R CELFILES. I have install R but I cannat asses the command: Data <- ReadAffy() and I got the error: Error in AllButCelsForReadAffy(..., filenames = filenames, widget = widget, : No cel filennames specified and no cel files in specified directory:C:/Documents and Settings/pawan.k/Desktop. Wit regds, Pawan ________________________________ This e-mail

Hi David and Mats, Thanks for your explanation. If my understanding is correct, it means we don't need to consider the side-effect of malloc/free unless compiling with -ffreestanding. Because without -ffreestanding, user defined malloc/free should be compatible with std library. It makes sense to me. My point is, in std library, malloc is allowed to return null if this malloc failed. Why

For help: Llvm generated instruction calls a function (extern), the function will have a SEH exception (EXCEPTION_ACCESS_VIOLATION), But JIT can not capture the exception of the EXCEPTION_ACCESS_VIOLATION. I saw Bug 24233. EXCEPTION_ACCESS_VIOLATION exception cannot be captured after modification. How to catch EXCEPTION_ACCESS_VIOLATION exceptions on win64 ? haifeng.qin at wellintech.com