User: Julian Lee

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Julian Lee140
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Posts by Julian Lee

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Answer: A: [R] easier way to print heatmap on multiple pages?
... Alternatively, you can output your heatmaps using the library, 'ctc'. Use TreeView or JavaTreeView to view those heatmaps. I find them more useful and easier than chopping up the PDFs. hope that helps. regards julian ----- Original Message ----- From: "Yannick Wurm" To: bioconductor at stat. ...
written 9.9 years ago by Julian Lee140
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Cannot Subset Columns in beadarray package, ExpressionSetIllumina Class in R-2.8.0, BioBase 2.2.1, beadarray 1.10.0
... Hi Mark and Others, I'm having some problems with the new beadarray package. I can't subset the columns, Example >library(beadarray) Loading required package: limma Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory mater ...
cancer beadarray written 10.3 years ago by Julian Lee140
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BMP4 probe '1940386' missing in illuminaHumanv2BeadID.db (as compared to illuminaHumanv2ProbeID.db)
... Hi Lynn and Marc, Thanks for your help and trying to get to the source of the problem. Perhaps BMP4, 1940386 is an anomaly. regards julian ----- Original Message ----- From: "Lynn Amon" To: "Marc Carlson" Cc: "Julian Lee" , "bioconductor" Sent: Monday, November 3, 2008 10:41:14 AM GMT -08:00 ...
annotation cancer probe annotate written 10.4 years ago by Julian Lee140
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Beadarray and illumina methylation arrays
... Hi Katrina and Mark, just a short comment. i'm also learning bits and pieces here, so correct me if i'm wrong. -Yes, currently the only way of reading methylation data into beadarray is by using the bead-level data. I've been working with some illumina Goldengate methylation datasets. (this is di ...
normalization cancer beadarray written 10.4 years ago by Julian Lee140
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BMP4 probe '1940386' missing in illuminaHumanv2BeadID.db (as compared to illuminaHumanv2ProbeID.db)
... Hi, may i know the differences between the 2 packages and why is this so. I have a gene of interest on the Illumina platform and have been using the IlluminaHumanv2ProbeID.db package to annotate it, but things have changed when i moved to R.2.8.0 on illuminaHumanv2BeadID.db package. I'll illustrat ...
cancer annotate written 10.4 years ago by Julian Lee140 • updated 10.4 years ago by Marc Carlson7.2k
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Answer: A: biomart doesn't annotate all the genes queried -CEACAM6
... Hi marc, thanks. I'm using the hgu133plus2.db package as a control to the biomaRt package. I think biomaRt has plenty of potential and gives users tremendous power in mapping across different organisms, databases etc. I'm quite certain I'll be using some of its functionality in future. regards j ...
written 10.5 years ago by Julian Lee140
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biomart doesn't annotate all the genes queried -CEACAM6
... Dear all, I'm having some problems trying to annotate some genes, eg. CEACAM6. My problem is as follows, Query input = chromosome numbers 1:22, Output attributes = ensembl_gene_id, unigene, chromosome_number,start_position,end_position,hgnc_symbol ##Code >require(biomaRt) >ensembl<-use ...
cancer hgu133plus2 annotate affy biomart written 10.5 years ago by Julian Lee140
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Answer: A: aCGH package - performance Issues
... Hi R, wonderful article. 8 algorithms in MPI. I would so love to test your code but unfortunately i do not have the luxury of a linux cluster here(that however can be fixed ;)). I do however have a Sun v490, 4 dual core UltraSparcIV++ with 32GB RAM. I presume it'll work on this SMP too, however ...
written 10.9 years ago by Julian Lee140
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aCGH package - performance Issues
... Hi all, I would like to know if there's a way to tweak the performance of the aCGH package, particularly the find.hmm.states function Input dataset Agilent CNV 31 samples 200,000 clones Hardware 2 Intel Xeon Dual Core 3GHz (total of 4CPUs) 4 GB RAM Windows 2003 Server Edition Software R version ...
snp cancer written 10.9 years ago by Julian Lee140
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Bioinformatics Positions, National Cancer Centre Singapore
... Bioinformatics Specialist (Genomic Oncology) Reference: NCC/CMR/0208/028 Posted Date: 25 Apr 08 You will be involved in the analysis and curation of genome-wide cancer information related to cancer, ranging from genotypes, copy number analysis, gene expression, and epigenetics. You will be expected ...
microarray epigenetics cancer written 10.9 years ago by Julian Lee140

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