User: Cornish, Joseph NIH/NIAID [F]

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Posts by Cornish, Joseph NIH/NIAID [F]

<prev • 5 results • page 1 of 1 • next >
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What is the FDR set to for the BH method.
... Suppose when I write the results of a microarray experiment fit using limma to file. In doing this I decide to adjust the p-values using the BH method for adjusting the p-values. As I understand it, this method assesses the significance of a result assuming some prior rate of false discovery (type 1 ...
microarray written 6.2 years ago by Cornish, Joseph NIH/NIAID [F]50 • updated 6.2 years ago by Naomi Altman6.0k
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Limma linear models
... I had a few quick questions about the limma models. The first is when writing these to a file, the fold changes would be the "Coef" column, not the A column, which is the average across all of the arrays? The second is when I write my bayes model to a file, it only attaches the probe ID, I wanted to ...
annotation limma written 6.5 years ago by Cornish, Joseph NIH/NIAID [F]50 • updated 6.5 years ago by Wu, Di120
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Comment: C: Heatmaps for Agilent Single Color 4x44k using limma and vsn.
... Hello Davis, I posted a simple example, which after fixing a problem in the longer example no produces the same results. I only posted the longer one because I wasn’t able to reproduce the results of the longer version initially. I’ve been sort of banging my head on this for a while so I mi ...
written 6.5 years ago by Cornish, Joseph NIH/NIAID [F]50
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Comment: C: Heatmaps for Agilent Single Color 4x44k using limma and vsn.
... Hello James, Are you referring to function names or constants? The constants are an old habit I picked up long ago in my CS classes, there are a ton but it makes them stand out for me in vim more readily. I've come to avoid camel case since switching to linux, it makes searching for things a nightm ...
written 6.5 years ago by Cornish, Joseph NIH/NIAID [F]50
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Heatmaps for Agilent Single Color 4x44k using limma and vsn.
... I am attempting to write a script that will allow me to do bulk benchmarking of various methods for normalization and background correction. I am concerned that I am not processing the data correctly and this may be leading to the abnormal heatmaps that I am seeing. For a test case, I am using an ex ...
annotation normalization vsn limma written 6.5 years ago by Cornish, Joseph NIH/NIAID [F]50 • updated 6.5 years ago by James W. MacDonald51k

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