User: Simon Lin

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Simon Lin270
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Posts by Simon Lin

<prev • 27 results • page 2 of 3 • next >
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BeadChip location info
... It is in the lumiHumanV1 or lumiHumanV2 annotation library. -Simon ==================================== Message: 17 Date: Mon, 4 Jun 2007 21:17:23 -0700 (PDT) From: Yu Chuan Tai Subject: [BioC] BeadChip location info. To: bioconductor at stat.math.ethz.ch Message-ID: Content-Type: TEXT/PLAIN; cha ...
annotation lumihumanv1 lumihumanv2 written 12.5 years ago by Simon Lin270
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Illumina BeadArray Annotation
... Hi Paul, We are making major overhaul of the annotation workflow. Previously, sequences from the FANTOM database were all reported as NA. To fix the problem, here is the new workflow: 1) The mapping from a 50-mer to a gene is done by BLAST. 2) The most recent release of the RefSeq (this week) is u ...
annotation cancer lumimousev1 lumi trigger written 12.5 years ago by Simon Lin270
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Gene orthologes lookup table
... Is there a orthologes lookup table between human, mouse, and (maybe rat)? Hopefully, all use Entrez Gene (LocusLink) ID? The EGO database by J.Q. utilizes the THC id; take some effort to parse out. Thanks! Simon ...
written 12.6 years ago by Simon Lin270 • updated 12.6 years ago by Sean Davis21k
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read a CEL file?
... There used to be a function in affy called readCelFile, which can read the pixel-level STDEV of the intensity measure of each square (probe) on the array. Nowadays it becomes readAffyBatch. Can we still get the image-level STDEV somehow? Thanks! ...
affy written 12.6 years ago by Simon Lin270 • updated 12.6 years ago by Ben Bolstad1.2k
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Student Intern Position, Summer 2007, Chicago, IL
... Student Intern Project, Summer 2007, Chicago, IL Although undergraduates are welcome, masters and PhDs in computational biology are preferrered. Robert H. Lurie Comprehensive Cancer Center of Northwestern University, downtown Chicago. For details, see http://www.basic.northwestern.edu/projects/SoC ...
cancer written 12.7 years ago by Simon Lin270
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Category/ summery student project
... Hi Lana, The MSigDB is a good source! We are planning to have a summer student working on a similar project, but using a different database. Maybe we can coordinate the efforts. Simon Message: 4 Date: Mon, 12 Mar 2007 14:39:54 -0700 From: "Lana Schaffer" Subject: Re: [BioC] Category To: Messag ...
category written 12.7 years ago by Simon Lin270
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geneSetTest() / GESA
... Dear Gordon, Is the geneSetTest() fast to calculate? Not sure if you used permutation test under the hood. For GSEA and GSA, sometimes we see artifacts when the size of the set is too small. Is the same true for geneSetTest? Thanks! Simon Date: Sun, 04 Mar 2007 18:51:00 +1100 From: Gordon Smyt ...
written 12.7 years ago by Simon Lin270 • updated 12.7 years ago by Gordon Smyth39k
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Illumina - Beadarray - Limma
... Here are some alternative codes for the data transformation and normalization process. We have compared its performance with log2-quantile, but not rank invariant.Note that VST transformation, unlike log2, can take negative values. However, our experience also suggest that background correction is o ...
microarray normalization limma process lumi written 12.7 years ago by Simon Lin270
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Illumina Data transformation and Normalization
... We are planning to release a package to take some Illumina-specific features for the data transformation (not log2) and normalization (not quantile) process. We are looking for beta testers before sending the package to Bioconductor. If you are interested, please send me an email to s-lin2 at north ...
normalization written 13.1 years ago by Simon Lin270
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PC/Mac version-checking inside of R
... Is there a function to determine which version of R you are running? For example, quartz() will work on Macs, but not on Windows. Thanks! Simon ...
written 13.2 years ago by Simon Lin270 • updated 13.2 years ago by Seth Falcon7.4k

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