User: Stan Smiley

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Stan Smiley70
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Posts by Stan Smiley

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BioC v1.7 and R version?
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20051121/ cb77a3b4/attachment.pl ...
written 13.9 years ago by Stan Smiley70 • updated 13.9 years ago by Seth Falcon7.4k
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probe alignment clustering
... I'm in the process of validating the annotation from Affymetrix, and positioning each 25mer probe on the genome (just mouse and human so far). I'm in a position now to use this positioning data to validate the affy annotated alignments, which I'm doing now. My challenge now is to settle on the best ...
annotation affy process written 14.5 years ago by Stan Smiley70 • updated 14.5 years ago by Sean Davis21k
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Opinions on LIMaS
... Apologies to all if this is off topic, but I don't know where else to post it so here goes... Has any used Laboratory Information Management for Array Systems (LIMaS) on Oracle with Affymetrix data? And if so, I would greatly appreciate your opinions on it, and or better alternatives to managing t ...
written 15.5 years ago by Stan Smiley70
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Quantile normalization vs. data distributions
... Greetings, I have been trying to find a quantitative measure to tell when the data distributions between chips are 'seriously' different enough from each other to violate the assumptions behind quantile normalization. I've been through the archives and seen some discussion of this matter, but didn' ...
normalization written 15.6 years ago by Stan Smiley70 • updated 15.6 years ago by Naomi Altman6.0k
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Limma and Affymetrix ?
... I have been looking for some examples of limma with Affymetrix data. There is a simple example in the documentation, but not a case study as with the dye swap experiments, and I am confused as to how to proceed with using limma on my data. I need to eventually analyze a 2^4 factorial experiment, b ...
limma written 15.7 years ago by Stan Smiley70
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Comment: C: gcrma vs. rma
... Well, I'm glad to say the qqplot of the rma vs gcrma is *not* straight after the analysis redo. Thank goodness! Thanks to all who provided me such quick and informative responses! I've got a lot to read up on now... :) Stan Smiley > -----Original Message----- > From: Zhijin Wu [mailto:zwu ...
written 15.8 years ago by Stan Smiley70
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gcrma vs. rma
... Sorry if this should have been sent directly to Zhijin Wu, but here goes... Is there another resource for learning what the gcrma package is all about? Like the theory/rationale behind it and why/how it is better than rma? I must be doing something wrong, but my rma expression levels are the same ...
gcrma written 15.8 years ago by Stan Smiley70 • updated 15.8 years ago by Ben Bolstad1.1k

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