search for: cgh

Hi, I would like some extra information on the 'cgh' package in R. I noticed that there isn't much activity regarding this package on the R and BioC mailing list (I googled it). I started using this package and I have few questions: 1/ As I have a custom tiling like array @8um features resolution (affy), I have a lot of probes to work...

...i have two arrays of genes names,one with180000 gene names and the other with 24000 gene names,I have to compare both of them for finding common names. I have both the arrays in .csv format.i loaded the files and tried to compare them using for and if loops but I got the error Error in Ops.factor(cgh[i, 1], cgh[j, 2]) : level sets of factors are different Please suggest me how to solve this problem or any other alternative procedure Thanks ramakanth Get the freedom to save as many mails as you wish. To know how, go to http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/to...

Hi All, I am trying to make R package using R 2.6.2 And I am getting following error. When I give R CMD check t1\ ---------- Making package t1 ------------ adding build stamp to DESCRIPTION making DLL ... making CGHseg_rewrite.d from CGHseg_rewrite.c making rowMedians.d from rowMedians.c making runavg.d from runavg.c gcc-sjlj -std=gnu99 -Ic:/R/R-2.6.2/include -O3 -Wall -c CGHseg_rewrite.c -o CGHseg_rewrite.o gcc-sjlj -std=gnu99 -Ic:/R/R-2.6.2/include -O3 -Wall -c rowMedians.c -o rowMedians.o gcc-...

Hi all, I'm new to R and I'm struggling to decipher an error message. Briefly, I am trying to use the pvclust package to do hierarchical clustering of some CGH data. The data is from the Progenetix CGH database. It is arranged as a table where each column is a single case and each row is a single chromosome band. The value in each cell is either 0, 1, 2, or -1. Corresponding to no change, gain, high level amplification, or loss respectively Based on the d...

Dear R users, I´m studying about Bayesian Statistics. In this context, please, anyone have some basic script of RJMCMC (Reversible Jump Markov chain Monte Carlo) in R or WinBUGS? My aim is to learn how to implement this methodology. Thanks a lot. Marcus Vinicius [[alternative HTML version deleted]]

...ould someone be kind enough to point it out because it isn't obvious to me. Although my data is from biological experiments I think my problem is with R rather than the nature of the data, but I may be wrong. I am attempting to use the pvclust package to do some hierarchical clustering on some CGH data I have downloaded from the Progenetix database (http://www.progenetix.de/~pgscripts/progenetix/Aboutprogenetix.html). The data is in tab delimited format, each column is a single sample each row is a chromosome band some example dummy data is shown below. band sample1 sample2 sample3 sa...

...======== All packages from the 1.3 release are included. All current bug fixes have been applied, and most have upgraded and provide enhanced functionality. SOME OF THE MAJOR UPGRADES FOR RELEASE 1.4: =========================================== -- Proteomics (PROcess, gpls, apComplex) -- Array CGH (DNAcopy, aCGH) -- Cell cycle analysis (GeneTS) -- Packages for lab assay analysis and management (prada) -- Agilent arrays handling in limma -- Annotation tools (Resourcer, GOstat, goTools, ontoTools) -- Improved interfaces (limmaGUI, affylmGUI, webbioc, -- MAGE file processing (RMAGEML) -...

...informatics approaches to discover, validate and generate therapeutics against molecular targets in oncology. We have generated large populations of tumors that exhibit inter-tumor heterogeneity similar to that seen in human tumor populations. Each tumor has been characterized by microarray, array CGH, histology, key signaling pathways as well as sensitivity to a variety of cancer therapeutics, including AVEO's clinical stage drug candidates. This well-characterized tumor population model system enables the correlation of gene expression and DNA copy number with drug efficacy, providing an...

...stimation and GAMMs by REML/PQL MLInterfaces Uniform interfaces to R machine learning procedures for data in Bioconductor containers multtest Resampling-based multiple hypothesis testing Neve2006 expression and CGH data on breast cancer cell lines nlme Linear and Nonlinear Mixed Effects Models nnet Feed-forward Neural Networks and Multinomial Log-Linear Models pamr Pam: prediction analysis for microarrays...

...ENABLE_DUMP > LLVM_DUMP_METHOD > void ValueTypeByHwMode::dump() const { > dbgs() << *this << '\n'; > } > +#endif > > ValueTypeByHwMode llvm::getValueTypeByHwMode(Record *Rec, > const CodeGenHwModes &CGH) { > -#ifndef NDEBUG > +#ifdef LLVM_ENABLE_DUMP > if (!Rec->isSubClassOf("ValueType")) > Rec->dump(); > #endif > > > thanks... > don > > The patch seems to be incomplete as it moves the failure to... [ 6%] Linking CXX executable ../../bin/...

Is anyone else seeing this bootstrap failure on current svn trunk? [ 6%] Linking CXX executable ../../bin/llvm-tblgen cd /sw/src/fink.build/llvm60-6.0.0-1/build/stage1/utils/TableGen && /sw/bin/cmake -E cmake_link_script CMakeFiles/llvm-tblgen.dir/link.txt --verbose=1 /sw/src/fink.build/llvm60-6.0.0-1/opt-bin/ccclang++ -fno-common -fPIC -fvisibility-inlines-hidden -Werror=date-time

...And do > Q.NH(summary(res)[[1]]$beta, x=0) To obtain the common transition matrix. Cheers, Oscar On 29/2/12 03:59, "monkeylan" <[hidden email]> wrote: > Dear Oscar, >   > I am extremely grateful to your help and detailed explanation of the use of > RJaCGH package. > But, when runing the sample codes you listed, another issue I am a little > confused is as following: > After runing summary(res), I have got the estimation of the random matrix > Beta: > > Parameters of the transition functions: >        Normal  Gain > No...

Hi, We have a central Samba server which works fine. It also supplies WINS services which work fine. It also builds a browse list which seems to work fine. However, when I open 'Entire Network' on my W95 desktop machine on another subnet, I only see the workgroups / hosts on my subnet. The 95 machine is pointing to the Samba server as a WINS server. If I change the workgroup of

...lueTypeByHwMode::dump() const { >>> dbgs() << *this << '\n'; >>> } >>> +#endif >>> >>> ValueTypeByHwMode llvm::getValueTypeByHwMode(Record *Rec, >>> const CodeGenHwModes &CGH) >>> { >>> -#ifndef NDEBUG >>> +#ifdef LLVM_ENABLE_DUMP >>> if (!Rec->isSubClassOf("ValueType")) >>> Rec->dump(); >>> #endif >>> >>> >>> thanks... >>> don >>> >>> &gt...

...lueTypeByHwMode::dump() const { >>> dbgs() << *this << '\n'; >>> } >>> +#endif >>> >>> ValueTypeByHwMode llvm::getValueTypeByHwMode(Record *Rec, >>> const CodeGenHwModes &CGH) >>> { >>> -#ifndef NDEBUG >>> +#ifdef LLVM_ENABLE_DUMP >>> if (!Rec->isSubClassOf("ValueType")) >>> Rec->dump(); >>> #endif >>> >>> >>> thanks... >>> don >>> >> >&gt...

...is << '\n'; >> >>> } >> >>> +#endif >> >>> >> >>> ValueTypeByHwMode llvm::getValueTypeByHwMode(Record *Rec, >> >>> const CodeGenHwModes >> >>> &CGH) >> >>> { >> >>> -#ifndef NDEBUG >> >>> +#ifdef LLVM_ENABLE_DUMP >> >>> if (!Rec->isSubClassOf("ValueType")) >> >>> Rec->dump(); >> >>> #endif >> >>> >> >>&g...

...t; *this << '\n'; >>>>> } >>>>> +#endif >>>>> >>>>> ValueTypeByHwMode llvm::getValueTypeByHwMode(Record *Rec, >>>>> const CodeGenHwModes >>>>> &CGH) { >>>>> -#ifndef NDEBUG >>>>> +#ifdef LLVM_ENABLE_DUMP >>>>> if (!Rec->isSubClassOf("ValueType")) >>>>> Rec->dump(); >>>>> #endif >>>>> >>>>> >>>>> thank...

...t; } >> >> >>> +#endif >> >> >>> >> >> >>> ValueTypeByHwMode llvm::getValueTypeByHwMode(Record *Rec, >> >> >>> const CodeGenHwModes >> >> >>> &CGH) >> >> >>> { >> >> >>> -#ifndef NDEBUG >> >> >>> +#ifdef LLVM_ENABLE_DUMP >> >> >>> if (!Rec->isSubClassOf("ValueType")) >> >> >>> Rec->dump(); >> >> >>...

...>>> } >>>>>>> +#endif >>>>>>> >>>>>>> ValueTypeByHwMode llvm::getValueTypeByHwMode(Record *Rec, >>>>>>> const CodeGenHwModes >>>>>>> &CGH) { >>>>>>> -#ifndef NDEBUG >>>>>>> +#ifdef LLVM_ENABLE_DUMP >>>>>>> if (!Rec->isSubClassOf("ValueType")) >>>>>>> Rec->dump(); >>>>>>> #endif >>>>>>>...

...>> >> >> >> >>> ValueTypeByHwMode llvm::getValueTypeByHwMode(Record *Rec, >> >> >> >>> const >> >> >> >>> CodeGenHwModes >> >> >> >>> &CGH) >> >> >> >>> { >> >> >> >>> -#ifndef NDEBUG >> >> >> >>> +#ifdef LLVM_ENABLE_DUMP >> >> >> >>> if (!Rec->isSubClassOf("ValueType")) >> >> >> >>>...