search for: dchip

Sources for versions of R as far back as 0.65, I believe, are available on CRAN. You can try to compile from source. Andy > From: Qun Shi > > Hi, > > I'm trying to use the version of dchip combined with R to > analyze my data. > I need R version 1.6 which fits for dchip as dchip manual said. So I > would appreciate a lot if someone could tell me where I could > find this > version and download? I'm using Windows 2000. > > Thanks, Jean > > Qun(Jean)...

...Sources for versions of R as far back as 0.65, I believe, > are available on > > CRAN. You can try to compile from source. > > > > Andy > > > > > From: Qun Shi > > > > > > Hi, > > > > > > I'm trying to use the version of dchip combined with R to > > > analyze my data. > > > I need R version 1.6 which fits for dchip as dchip manual > said. So I > > > would appreciate a lot if someone could tell me where I could > > > find this > > > version and download? I'm using Windo...

Happy new year to all; A few days ago, I posted similar problem. At that time, I found out that our R program had been 32-bit compiled, not 64-bit compiled. So the R program has been re-installed in 64-bit and run the same job, reading in 150 Affymetrix U133A v2 CEL files and perform dChip processing. However, the memory problem happened again. Since the amount of physical memory is 64GB, I think it should not be a problem. Is there anyway we can configure memory usage so that all physical memory can be utilized? Our system is like this: System type: IBM AIX Symmetric Multiprocessin...

Hi.... I have a question about how to increase my memory size, could someone answer it for me?? I am using Bioconductor in R to calculate gene expression values with mas5, dchip, and mas4. I have only 18 samples, all from Affymetrix U133A Plus 2 arrays, which has ~54,000 genes. My machine equipments are: CPU P4 3.0GHz, and 1GM RAM. Somehow when I was running mas5 in R, it always showed the error message: "Cannot allocate vector of size 211702 Kb." I believed that...

I use dChip and Affymetrix gtype to apply some genotyping functions to some microarrays data. Do you know if similar R functions exist? Thank you! Francesco ----------------------------------------------------------- Francesco Falciano, Ph.D. CINECA (High Performance Systems) via Magnanelli, 6/3 40033 Casale...

I have just spent a day trying to determine why I seemed to be unable to read a file of microarray expression results into R properly. The file was produced by the Dchip software developed by Li and Wong at Harvard's Department of Biostatistics. It contains rows of tab-delimited fields in the order Probe set identifier Probe set description Array 1 expression Array 1 call Array 2 expression Array 2 call ... plus an extra tab (which I think is due to a progra...

...lly, I have a rare opportunity to run R in a system with 64GB memory without any limit on memory usage for any person or process. However, I encountered the memory problem error message like this: Error: cannot allocate vector of size 594075 Kb I got this error message while I was trying to apply dChip preprocessing procedures for 150 Affymetrix U133v2 chips that has > 22,000 probe sets on them. The actual codes I ran was like this: > Data <- ReadAffy(filenames = paste(HOME, "CelData/", fname, sep="")) > mem.limits() nsize vsize NA NA > gc() us...

...o the preprocessing respectively. Yet in this case, the results of background correction or normalization are not desirable, because not all the information known (namely 109 samples) is used to obtain a baseline or something like that. An alternative approach would be to pre-process the data in dChip, and then export it into R. Yet I am thinking about an approach that relies solely on R. Would you please give some suggestions on this issue, though it might be more a technical problem than a scientific (statistical) one? Much thanks for your help! look forward to your reply! All the best to y...