User: Chao-Jen Wong

gravatar for Chao-Jen Wong
Chao-Jen Wong580
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580
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USA/Seattle/Fred Hutchinson Cancer Research Center
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2 years, 8 months ago
Joined:
8 years, 3 months ago
Email:
c****@fhcrc.org

Posts by Chao-Jen Wong

<prev • 59 results • page 1 of 6 • next >
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gmapR: GsnapParam, does is support the --splicesites (-s) flag
... I am using GsnapParam to construct the parameter before using the gsnap function. I have the intron-level splicing in a file (L42.intron) that looks like: >AF117653.intron1 AF117653:12113..12250 >AF117653.intron2 AF117653:12337..12704   I would like to detect splices from this file but don' ...
gmapr written 2.8 years ago by Chao-Jen Wong580
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Answer: A: Error: cannot allocate vector of size 618.0 Mb
... Have you tried the command gc(reset=TRUE)? It seems you have enough RAM but too segment. You can first try gc(reset=TRUE) to reset the maximum space. If it still doesn't work, restart your computer. Cheers, Chao-Jen ----- Original Message ----- From: "???" To: bioconductor at r-project.org Sent: ...
written 5.0 years ago by Chao-Jen Wong580
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Answer: A: Repitools/ClusterPlots
... Hi, Gilian As Vince mentioned, the Repitools package doesn't exist in R 2.13 branch, but in R 2.14. It is just recently released as version 1.0.0. Anyhow, clusterPlots() was deleted from the package prior to its release and the authors haven't taken out the examples related to clusters from the vig ...
written 6.0 years ago by Chao-Jen Wong580
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Answer: A: lumi: Methylation450 Data Input
... Hi, Jiayi, Your "FinalReport.txt" (I guess it is the sample profile output containing methylation data and other annotation columns) is sufficient to create a MethyLumiM (not LumiBatch) class object. If you wish to perform QC control and preprocess the data, you will need to export the control prob ...
written 6.0 years ago by Chao-Jen Wong580
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Customizing gplots heatmap.2 - color range for heatmap and legend for RowSideColors
... Hi, Kurinji 1. *adjusting color range on heatmap.2* You can use the mighty "breaks" argument to symmetrically bin your data, ranged from 0 to 1, into color. For instance, bk <- seq(0, 1, by=0.025) heatmap.2(z.ma, breaks=bk, col=greenred, blah, blah) It should map values around 0.5 to black co ...
cancer convert written 6.0 years ago by Chao-Jen Wong580
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Comment: C: pckg Resourcerer : can't read "affy_HG-U133_Plus_2.zip" with getResourcerer()
... Hi, Guillaume, It seems likely a bug in the package. If you just need the annotation of affy HGU133 plus 2, you can simply install the hug133plus2.db package. See more detail, visit http://bioconductor.org/packages/release/data/annotation/html/hgu133 plus2.db.html Chao-Jen -- Chao-Jen Wong Pro ...
written 6.3 years ago by Chao-Jen Wong580
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Comment: C: Probe ID to Sequence
... Good to know! Thanks!!! Wondering why they are not exported for they are important information for filtering purposes. Cheers, Chao-Jen ----- Original Message ----- From: "Tim Triche, Jr." To: "Chao-Jen Wong" Cc: "khadeeja ismail" , bioconductor at r-project.org Sent: Monday, August 1, 2011 2:25 ...
written 6.3 years ago by Chao-Jen Wong580
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Answer: A: Probe ID to Sequence
... Hi, Khadeeja, Accession number and regulatory group can be found in IlluminaHumanMethylation450k.db. Unfortunately this database package does not have snp10. The easiest way I found is exporting those information (snp10 and UCSC refname) along with the probe intensity data from GenomeStudio. If an ...
written 6.3 years ago by Chao-Jen Wong580
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Answer: A: export lumimethyN object??
... Hi, Jasreet, Suppose x.lumi.n is the object returned by lumiMethyN or lumiMethyR or any lumuMethy related methods, i.e., > x.lumi.n <- lumiMethyN(blah blah ...) You can save this R object to an rda file: > save(x.lumi.n, file="x.lumi.n.rda") Next time when you want to work with x.lumi.n ...
written 6.3 years ago by Chao-Jen Wong580
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which illumina annotation package I should use for Illumina Mouse Ref 8 v 1.1 expression beadchip
... Dear list, I am not sure which illumina annotatin package I should use for Illumina Mouse Ref 8 v 1.1 expression beadchip. Is illuminaMousev2.db (GW6 v2) appropriate? At first I thought illuminatMouse GW6 format version 1 (illuminaMousev1.db) would include Mouse Ref-8 v1.1 probe annotation, but the ...
cancer written 6.4 years ago by Chao-Jen Wong580 • updated 6.4 years ago by Mark Dunning1.0k

Latest awards to Chao-Jen Wong

Great Question 2.7 years ago, created a question with more than 5,000 views. For Customizing gplots heatmap.2 - color range for heatmap and legend for RowSideColors
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Customizing gplots heatmap.2 - color range for heatmap and legend for RowSideColors

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