search for: hgu95av2

I downloaded: http://www.bioconductor.org/data/metaData/hgu95av2_1.7.0.tar.gz described as: Package: hgu95av2 Title: A data package containing annotation data for hgu95av2 Version: 1.7.0 Created: Wed Jan 12 16:57:23 2005 Author: Lin,Chenwei Description: Annotation data file for hgu95av2 assembled using data from public data re...

...hics Devices and Support for Colours and Fonts grid The Grid Graphics Package GSEABase Gene set enrichment data structures and methods hgu133a Affymetrix Human Genome U133 Set Annotation Data (hgu133a) hgu95av2 Affymetrix Human Genome U95 Set Annotation Data (hgu95av2) hgu95av2.db Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) hgu95av2cdf hgu95av2cdf KEGG A data package containing ann...

..."affydata" "affyPLM" "affyQCReport" [5] "annaffy" "annotate" "Biobase" "biomaRt" [9] "Biostrings" "DynDoc" "gcrma" "genefilter" [13] "geneplotter" "GenomicRanges" "hgu95av2.db" "limma" [17] "marray" "multtest" "vsn" "xtable" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11' Error in if (ok) { : missing...

...t;1690128" "4850681" "110433" "2640544" "4900370" "1430280" IEA NAS TAS IEA "6110044" "1170615" "6590546" "1690632" $`GO:0000052` [1] NA goG=sapply(test.goP,getSYMBOL,data="hgu95av2") error: "Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs " In this the 14th element has missing values, thus getSYMBOL raises issues. GetSYMBOL has to be given a char array, so a simple solution is infact to delete the missing elem...

...es: [1] "affy" "affydata" "affyPLM" "annaffy" "annotate" [6] "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter" [11] "geneplotter" "hgu95av2.db" "limma" "marray" "matchprobes" [16] "multtest" "ROC" "vsn" "xtable" "affyQCReport" Anything that I install after this gives me the same error. I tried uninstalling...

...ges: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" [9] "base" other attached packages: Rgraphviz geneplotter XML GOstats Category hgu95av2 KEGG multtest xtable "1.11.9" "1.11.8" "0.99-8" "1.6.0" "1.4.1" "1.12.0" "1.8.1" "1.11.2" "1.3-2" RBGL annotate GO graph Ruuid...

Hi, I have the following data frame: > print(mydatframe) __DATAFRAME__ V1 V2 V3 1 1007_s_at DDR1 discoidin domain receptor tyrosine kinase 1 2 1053_at RFC2 replication factor C (activator 1) 2, 40kDa 3 117_at HSPA6 heat shock 70kDa protein 6 (HSP70B') __END__ Is there a way to create a hash with V2 as Key and V3 as its value? - Gundala Viswanath Jakarta - Indonesia

...> >Attaching package: 'xtable' > > > The following object(s) are masked from package:graph : > > label > >Loading required package: multtest >Loading required package: Category >Loading required package: KEGG >Loading required package: hgu95av2 >Warning message: >affycoretools contains no vignette, nothing is added to the menu bar in: >addVigs2WinMenu("affycoretools") > > > sessionInfo() >Version 2.3.1 (2006-06-01) >i386-pc-mingw32 > >attached base packages: >[1] "splines" "tool...

...S.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu95av2.db_2.2.12 ALL_1.4.4 ExpressionView_0.1 [4] caTools_1.9 bitops_1.0-4.1 KEGG.db_2.2.5 [7] GO.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 [10] eisa_0.1 genefilter_1.24.2 Category_2.10.0 [13] AnnotationDbi_1.6.0 Biobase_2.4.1 isa2_0.1 loaded via a namesp...

...> params.chiptype <- pdnn.params.chiptype(energy.file, probes.pack = "hgu133aprobe") Calculating chip type specific parameters, (may take some time)... | | |Error in object$call : $ operator not defined for this S4 class > After this, I also tried to do it for hgu95av2 array as described in the package manual- > library(affypdnn) Loading required package: affy Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase&quo...

...and varMetadata description: sex: Female/Male type: Case/Control score: Testing Score featureData featureNames: AFFX-MurIL2_at, AFFX-MurIL10_at, ..., 31739_at (500 total) fvarLabels and fvarMetadata description: none experimentData: use 'experimentData(object)' Annotation: hgu95av2 # what I would like to allow in use: (subset2 = subset(expressionSet, sex=="Male", score > 0.75) # note the == instead of = [[alternative HTML version deleted]]

...: chr [1:2] "featureNames" "featureColumns" > .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots > .. .. .. .. ..@ .Data:List of 1 > .. .. .. .. .. ..$ : int [1:3] 1 1 0 > ..@ annotation : chr "hgu95av2" > ..@ protocolData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots > .. .. ..@ varMetadata :'data.frame': 0 obs. of 1 variable: > .. .. .. ..$ labelDescription: chr(0) > .. .. ..@ data :'data.frame...

...or computational biology and bioinformatics" by Robert C Gentleman et al., 2004. Generating Heatmaps till Fig2 is working so I think esetSel is not the problem.. However, for generating the Figure 3, for GO annotations the following command is not working: > ll <- mget(geneNames(esetSel),hgu95av2LOCUSID)    #it is displaying error messages  Error in mget(geneNames(esetSel), hgu95av2LOCUSID) : object 'hgu95av2LOCUSID' not foundand also geneNames not found try featureNames instead Hence I cant proceed to the next set of commands provided in the paper which are as follows: > ll <...

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

Hi, I was installing hundreds of packages on a machine with a single call to install.packages() and after a long time the call to install.packages() finally returned with the following warnings and errors: Warning messages: 1: packages ?hgu133aprobe?, ?hgu95av2.db?, ?BSgenome.Celegans.UCSC.ce2?, ?BSgenome.Mmusculus.UCSC.mm10?, ?BSgenome.Dmelanogaster.UCSC.dm3.masked?, ?BSgenome.Hsapiens.UCSC.hg18.masked?, ?BSgenome.Hsapiens.UCSC.hg19.masked?, ?BSgenome.Mmusculus.UCSC.mm9.masked?, ?BSgenome.Scerevisiae.UCSC.sacCer2?, ?BSgenome.Hsapiens.NCBI.GRCh38?,...