User: Simon Lin

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Simon Lin270
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Posts by Simon Lin

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What should happen to control probe information in beadlevel Illumina analyses?
... Hi Alice, Reasonable to exclude them from analysis. In a hypothesis-testing framework, you can ignore all the control probes, because we are not interested in their differential expression at all. If you choose to include them, it is an empirical way to empirical your false discovery rate, because ...
probe written 11.6 years ago by Simon Lin270
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What should happen to control probe information in bead level Illumina analyses?
... Hi Alice, Please check the expression level of these negative control probes. They must be very low. If all the negative control probes are high, you might get a hybridizatin problem; check the stringency control probes. If these low-expressed negative controls are in your Top50 lists, you might t ...
probe written 11.6 years ago by Simon Lin270 • updated 11.6 years ago by Johnstone, Alice410
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tweaks for the heatmap ()?
... I am looking for two tweaks of the heatmap function: 1) a choice to order the genes by 1-D MDS projection. The current hierarchical clustering flips many nodes. 2) a color bar at the side to indicate the color scale, as with maColorBar() in the marray package Any code to share? Thanks! Simon ...
clustering marray written 12.0 years ago by Simon Lin270 • updated 11.9 years ago by Aedin Culhane510
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rule of MM design on Affymetrix?
... What is the rule of the MM desing on the Affymetrix array? I think it is a one-basepair change in the middle, but how exactly? A-> C T->G, C->T G->A? Many thanks, Simon ...
written 12.0 years ago by Simon Lin270 • updated 12.0 years ago by James W. MacDonald51k
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Answer: A: About between-array normalization in limma
... Sean Davis Wrote: >The rule-of-thumb is that if you are working with two-color data and >using ratios only, then you probably do not need between-array >normalization. What is the rationale behind this claim? Is it because the common ref channel serves as kind of internal calibration contr ...
written 12.0 years ago by Simon Lin270
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GO analysis code snippet
... Hello, I am looking for some GO analysis code-snippet for the following task, 1) list all the GO terms under "molecular function" 2) For a given GO id, list the associated Entrez gene IDs (or Affymetrix probe IDs for U133A) A further question: is there a package analyzeing GO hierarchically? I me ...
go written 12.2 years ago by Simon Lin270 • updated 12.2 years ago by Seth Falcon7.4k
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Answer: A: from RefSeq to GO terms / gene symbol to geneID
... If you do not have a large number of sequences, BioMart is a good choice. -Simon ----- Original Message ----- From: "Lina Hultin-Rosenberg" To: "Simon Lin" Cc: ; Sent: Friday, June 29, 2007 12:54 AM Subject: Re: [BioC] from RefSeq to GO terms / gene symbol to geneID > Dear Simon and Sean, & ...
written 12.3 years ago by Simon Lin270
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Bioconductor Digest, Vol 52, Issue 18
... We have evaluated the methods in Lumi using the MAQC benchmark data. The publication is under review. Pan, can you add the inter-lab concordance comparison results (Three curves: raw, Beadstudio, and lumi) in the lumi manual? Thanks! Simon ================ Date: Tue, 19 Jun 2007 11:42:43 +0200 Fr ...
normalization lumi written 12.3 years ago by Simon Lin270
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from RefSeq to GO terms / gene symbol to geneID
... In the following two unrelated messages, both Sean and Nianhua suggested to download and parse some data tables from the NCBI. The gene_info and several other tables seems very useful. If that is the case, why not have it pre-loaded into a SQlite and distribute it as part of the annotation package f ...
proteomics coverage annotation go written 12.4 years ago by Simon Lin270
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Answer: A: Memory issue in 500k chip analysis
... We are experiencing a similar memory problem with Illumina SNP chips. We are looking for a general solution using databases to handel very large data sets. Does that make sense? -Simon Date: Thu, 7 Jun 2007 11:43:51 +0200 From: Olivier Nu?ez Subject: [BioC] Memory issue in 500k chip analysis To: ...
written 12.4 years ago by Simon Lin270

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