User: Vladimir Morozov

Reputation:
130
Status:
Trusted
Location:
Last seen:
4 years, 8 months ago
Joined:
9 years, 7 months ago
Email:
v*******@als.net

Posts by Vladimir Morozov

<prev • 13 results • page 1 of 2 • next >
0
votes
0
answers
379
views
0
answers
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 4.7 years ago by Vladimir Morozov130
0
votes
1
answers
412
views
1
answers
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 6.6 years ago by Vladimir Morozov130
0
votes
1
answers
412
views
1
answers
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 6.6 years ago by Vladimir Morozov130
0
votes
1
answer
412
views
1
answer
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 6.6 years ago by Vladimir Morozov130 • updated 6.6 years ago by Gregoire Pau310
0
votes
0
answers
406
views
0
answers
'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 7.8 years ago by Vladimir Morozov130
0
votes
1
answer
292
views
1
answer
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 8.0 years ago by Vladimir Morozov130 • updated 8.0 years ago by Marc Carlson7.2k
0
votes
2
answers
405
views
2
answers
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 9.5 years ago by Vladimir Morozov130
0
votes
1
answer
429
views
1
answer
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 9.5 years ago by Vladimir Morozov130 • updated 9.5 years ago by Marc Carlson7.2k
0
votes
1
answer
476
views
1
answer
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 9.5 years ago by Vladimir Morozov130 • updated 9.5 years ago by Martin Morgan ♦♦ 20k
0
votes
1
answers
244
views
1
answers
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 9.6 years ago by Vladimir Morozov130

Latest awards to Vladimir Morozov

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 302 users visited in the last hour