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User: Park, Richard

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Park, Richard220
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14 years, 6 months ago
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r***********@joslin.harvard.edu

Posts by Park, Richard

<prev • 22 results • page 1 of 3 • next >
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Answer: A: GOstats: another problem
... Is there any easy way to output the results of get("GO:0003824", GOMFOFFSPRING) for example. I have tried using the standard output functions write, and write.table, is there any easy way to output really long lists? thank, Richard -----Original Message----- From: John Zhang [mailto:jzhang@jimmy. ...
written 14.6 years ago by Park, Richard220
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Answer: A: Expression on different Affy arrays
... Hi Donglei, I think using MAS 5 is a perfectly reasonable way to go w/ out being able to use rma to a complete background normalization. I would just be careful about trying to deduce signifigance from genes w/ lower expression and lower fold change values. This kind of analysis would need to be bro ...
written 14.7 years ago by Park, Richard220
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Answer: A: large amount of slides
... Hi Vada, I would caution you on doing rma on that many datasets. I have noticed a trend in rma, that things get even more underestimated as the number and variance of the data increases. I have been doing an analysis on immune cell types for about 100 cel files. My computer (windows 2000, 2gb of ram ...
written 14.7 years ago by Park, Richard220
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Answer: A: supervised clustering
... Dear Steve, In our lab, we have found this implementation of clustering quite useful. It is based on the work of Michael Eisen at Stanford. This version is a faster implementation of the various clustering methods. It has mainly unsupervised clustering methods but also include various implementatio ...
written 14.7 years ago by Park, Richard220
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Answer: A: Question on afy/gcrma probe indexes
... Hello, I have tried to access the x and y coordinates using xy2i() and i2xy() functions. I would be very cautious about the values you get from these functions. I tried creating a fake .cel file using these functions and the result was never fully correct. I eventually had to download some library ...
written 14.8 years ago by Park, Richard220
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large data set correlations?
... Hi Everyone, this is a post to get some ideas on ways to approach large data set analyses. For instance, I have over 100+ affymetrix chips organized into 23 different categories of cell types. So basically it is a matrix with 23 columns and 12500 rows. What methods would people suggest to correlate ...
probe written 15.1 years ago by Park, Richard220
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Answer: A: Probe Cell
... I've had problems using xy2indices function, but to get a list of all the x and y locations for the hg_u95av2 chip, you can go and download the cdf file from: http://www.affymetrix.com/support/technical/libraryfilesmain.affx (you may need to register for affymetrix's website, which is free) You ca ...
written 15.3 years ago by Park, Richard220
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Answer: A: microarray data representation
... Hi Cass, I've done something similar to what you are looking to do. My PI and I decided on our own formats as compared to exprset to make it easier for the standard biologist to use. If you are thinking of a java interface into R, you may want to look into dcom automation server. I have made a visua ...
written 15.3 years ago by Park, Richard220
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Anyone Know how to make a fake CEL file?
... Hi Johannes, I am going to try and use real values from experimental cel files to make various fake cel files w/ varying percentages of genes changing over time; i.e. having 20% of the genes change w/ a 2-5 fc by the third time point. The point of all of this is to try and understand what happens du ...
normalization cdf probe affy written 15.4 years ago by Park, Richard220 • updated 15.4 years ago by mai98ftu@studserv.uni-leipzig.de140
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Anyone Know how to make a fake CEL file?
... I am trying to make a couple of fake cel files to represent a time course treatment between three time points. I am trying to test the effects of normalization on various possible treatments. Is there a way to make a fake CEL file? and if there is, how do you know the corresponding x and y locations ...
normalization cdf affy written 15.4 years ago by Park, Richard220 • updated 15.4 years ago by Laurent Gautier2.2k

Latest awards to Park, Richard

Popular Question 14.6 years ago, created a question with more than 1,000 views. For mt.teststat
Popular Question 14.6 years ago, created a question with more than 1,000 views. For P values on Log or Non-Log Values

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