User: Park, Richard

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Park, Richard220
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Posts by Park, Richard

<prev • 22 results • page 2 of 3 • next >
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Seeking collaboration for an opensource data analysisinterface project
... Hi Andrea, I have spent sometime trying to create microarray analysis interfaces between visual basic to R/S-plus/ArrayAnalyzer. What types of platforms were you thinking of using to implement this idea? I have found that creating interfaces in s-plus is sort of cumbersome and hard to adapt for mult ...
microarray affy written 16.0 years ago by Park, Richard220
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Re: offer from I Neuhaus to create a BMS response; keep incore, please
... Hi Everyone, I was just talking with my PI the other day and he told me that he had an interesting conversation with one of the lead developers at affymetrix. I know there have been discussions about affy's move toward a binary format and how this will affect open source environments such as biocond ...
go affy written 16.1 years ago by Park, Richard220
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Answer: A: Re: location in chromosome
... hi, you should take a look at the annotate() package. chromLoc-class Class chromLoc, a class for describing the location of a gene on a chromosome. chromLocation-class Class chromLocation, a class for describing genes and their chromosome mappings. I haven't dealt much with chromosome locations, I ...
written 16.2 years ago by Park, Richard220
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Answer: A: normalize by or across all treatments
... These are my two cents to the question. I would at first normalize everything together via rma, which does poses risks of diminishing or enhancing treatment effects. But I believe this would allow you to see the overall picture of the data and give you a general sense of how each treatment compares ...
written 16.2 years ago by Park, Richard220
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Answer: A: chips A,B and C
... Hi Nicolas, Yes, I agree with Jim, since the 3 chips are testing different sets of genes, it is not necessarily that important to normalize everything together, since expression values in microarrray's are relative. But I can see the need of normalizing everything together if you are trying to link ...
written 16.2 years ago by Park, Richard220
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Answer: A: Adding chips to an existing set of normalised data
... Hi Rafael, I was just wondering if you could give me your opinion on my method of normalization. I was always under the impression that it is best to always renormalize the entire data set whenever you add or remove an additional chip. This would correspond to your 0 method. I do understand that thi ...
written 16.2 years ago by Park, Richard220
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Answer: A: Affy vs. cDNA : Low and not expressed genes
... Dear Adai, I can not tell you what is the correct way of doing analysis, but maybe I can give you a little insight by telling you how I do analysis on my own chips. I am computational biologist and I have been doing most of my labs microarray analysis for the past year. We use affymetrix chips in o ...
written 16.2 years ago by Park, Richard220
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Replicate Analysis
... Hello everyone, I was wondering if anyone knew of a function within bioconductor or method to provide some sort of metric for replicate quality analysis. I have typically been using multipanel graphs (having each replicate plotted vs each other) to get a sense of the replicate qualities. However, I ...
written 16.2 years ago by Park, Richard220
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P values on Log or Non-Log Values
... Hi Everyone, I am currently using the mt.teststat to calculate p-values between various samples. I was wondering if anyone knew if it was ok to run p-values on logged or non-logged values? In the past using MAS processing, I always calculated pvalues on the raw values, however I have recently switch ...
written 16.3 years ago by Park, Richard220 • updated 16.3 years ago by James W. MacDonald50k
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Probe Level Expression
... Dear Everyone, Could someone please point me to the function within Bioconductor that allows me to see the individual expression values for each of the probes on a chip? I have a specific probe I want to look at and I would like to see the 12-20 perfect match and mismatch pairs for that probe id. T ...
probe written 16.3 years ago by Park, Richard220 • updated 16.3 years ago by Laurent Gautier2.2k

Latest awards to Park, Richard

Popular Question 15.1 years ago, created a question with more than 1,000 views. For mt.teststat
Popular Question 15.1 years ago, created a question with more than 1,000 views. For P values on Log or Non-Log Values

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