User: Vladimir Morozov

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Posts by Vladimir Morozov

<prev • 13 results • page 1 of 2 • next >
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Is it possible to get SRA sample attributes for a given sample or experiment ID?
... Hi, Is it possible to get SRA sample attributes for a given sample or experiment ID? Here is the sample http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?sample=SRS388155. With SRAdb package: > dbGetQuery(sra_con,"select * from sample where sample_accession = 'SRS388155' ") sample_ID sample_alias ...
sradb written 5.2 years ago by Vladimir Morozov130
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Comment: C: EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormo
... Henrik, I think you make the right guess. Anyway the tiff file is 0500101820.0.tif - https://docs.google.com/leaf?id=0B2NLCeM3RRN2ODIxYW VmZjItYzYwNS00YjJjLWE2YjQtYjQwZGUzZTJkOTBi&hl=en Thanks, Vlad -----Original Message----- From: henrik.bengtsson@gmail.com [mailto:henrik.bengtsson@gmail. ...
written 7.2 years ago by Vladimir Morozov130
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Comment: C: EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormo
... Hi Gregory, It dosen't seem to be multiple version problem: [rstats:ImageAnal] ldd /usr/local/lib64/R/library/EBImage/libs/EBImage.so|grep -i magic libMagickCore.so.3 => /usr/lib64/libMagickCore.so.3 (0x00007f264092f000) libMagickWand.so.3 => /usr/lib64/libMagickWand.so.3 (0x ...
written 7.2 years ago by Vladimir Morozov130
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EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormode),
... Hi, I get image reading error: > x <- readImage( "/data/projects/ImageAnal/tiff/0500101820.0.tif" ) Error in .Call("lib_readImages", as.character(files), as.integer(colormode), : negative length vectors are not allowed > packageVersion('EBImage') [1] '3.6.0' > ImageMagic can wo ...
convert written 7.2 years ago by Vladimir Morozov130 • updated 7.2 years ago by Gregoire Pau310
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'ArrayExpress' creates invalid AffyBatch objects
... Hi, There are the errors from object check > validObject(ab) Error in validObject(ab) : invalid class "AffyBatch" object: 1: feature numbers differ between assayData and featureData invalid class "AffyBatch" object: 2: featureNames differ between assayData and featureData > length(feature ...
written 8.4 years ago by Vladimir Morozov130
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org.Hs.eg "gene_info" table seems to be worng
... Hi, org.Hs.eg "gene_info" table seems to be worng > conn <- org.Hs.eg_dbconn() #the example seems correct > dbGetQuery(conn, "SELECT * FROM gene_info LIMIT 3;") _id gene_name symbol 1 1 alpha-1-B glycoprotein A1BG 2 2 alpha-2-macrog ...
go written 8.5 years ago by Vladimir Morozov130 • updated 8.5 years ago by Marc Carlson7.2k
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Answer: A: GSEABase how to map gene symbols to mouse EntrezId or Affy
... Martin, You are right that disagreement beween human and mouse symblos is the problem. But you still should get some mapping if translate symbols into capwords > sum(!is.na(mget(gss[[1]]@geneIds,org.Mm.egSYMBOL2EG,ifnotfound=NA))) [1] 0 > sum(!is.na(mget(capwords(tolower(gss[[1]]@geneIds)),or ...
written 10.1 years ago by Vladimir Morozov130
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GSEABase how to map gene symbols to mouse EntrezId or Affy
... Hi Any suggestions how to map gene symbols to mouse EntrezId(preffered) or Affy. mapping to Entez apparently is not supported by GSEABase > mapIdentifiers(gss,EntrezIdentifier()) Error in .mapIdentifiers_isMappable(from, to) : unable to map from 'Symbol' to 'EntrezId' neither GeneIdentifi ...
written 10.1 years ago by Vladimir Morozov130 • updated 10.1 years ago by Marc Carlson7.2k
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GSEABase error in parsing msigdb_v2.5.xml
... Hi, I get error reading the last vesrsion of Broad msigdb . Is it supposed to work? > gss <- getBroadSets('/data/PathDB/msigdb_v2.5.xml') Error: 'getBroadSets' failed to create gene sets: invalid BroadCollection category: 'c5' > traceback() 6: stop("'getBroadSets' failed to create gene ...
go infrastructure hgu95av2 biobase ruuid annotationdbi written 10.1 years ago by Vladimir Morozov130 • updated 10.1 years ago by Martin Morgan ♦♦ 21k
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Comment: C: advice in building GOALLENTREZID {GO}
... > Yes, but if you do, and you want to use any other annotation, you must also build that. The annotation packages are inter-connected in non-trivial ways (many depending on GO), so mixing and matching is not a simple process, which is pretty much why we don't do it more often. Essentially I ne ...
written 10.2 years ago by Vladimir Morozov130

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