User: Jabez Wilson

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Jabez Wilson150
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Posts by Jabez Wilson

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Comment: C: use of duplicateCorrelation in Limma with agilent one-color arrays
... Thank you, Gordon, for your help. (coef obviously should be '1' not '-1') Jabez ...
written 7.7 years ago by Jabez Wilson150 • updated 4.7 years ago by Gordon Smyth38k
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Comment: C: use of duplicateCorrelation in Limma with agilent one-color arrays
... Dear Gordon, thank you for your comments. I am new to single color arrays, having used limma extensively with two-color in the past. I admit I have borrowed heavily with my coding from the mattick lab wiki http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarray_data_with ...
written 7.7 years ago by Jabez Wilson150 • updated 4.7 years ago by Gordon Smyth38k
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use of duplicateCorrelation in Limma with agilent one-color arrays
... Hi, everyone, I am using limma to analyse an agilent one-color array experiment, and have run into difficulties with duplicateCorrelation. My experiment is as follows: single color agilent arrays, 4 WT samples, and 3 samples of each of 4 treatment (treatments 1-4). I also have technical replicates ( ...
limma process written 7.7 years ago by Jabez Wilson150 • updated 7.7 years ago by Gordon Smyth38k
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Answer: A: limma data frame subsetting problem
... Yes, thanks, Axel, I think that may well do the trick - assuming you meant rowMaxs() ;-) You're right, it is an RGList not a DF. Jab --- On Wed, 5/10/11, axel.klenk@actelion.com wrote: From: axel.klenk@actelion.com Subject: Re: [BioC] limma data frame subsetting problem To: "Jabez Wilson" C ...
written 8.0 years ago by Jabez Wilson150
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limma data frame subsetting problem
... Dear Bioconductors, I want to do something simple, which I cannot find the solution to. I have a limma data frame and I want to select a subset of the data frame based on whether the values in the "G" channel are > e.g. 5000 As an example I use swirl data targets <- readTargets("SwirlSamp ...
limma written 8.0 years ago by Jabez Wilson150
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using vsn to normalize protein array data
... I'd like to use the vsn package to normalize protein array data, as described in "Felgner et al 2009 PNAS 106:13499-13504 A burkholderia psuedomallei protein microarray reveals serodiagnostic and cross- reactive antigens". I have a set of "positive" and "negative" samples labelled with Cy3 and read ...
microarray vsn written 8.1 years ago by Jabez Wilson150 • updated 8.1 years ago by Wolfgang Huber13k
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Answer: A: Limma analyse factorial data with two-color arrays
... Thanks for that suggestion, Naomi, I take it you mean "separate" channel analysis in the limma users guide. There's a complication, in that there are technical dye-swap replicates for each sample - I can't currently see how I can integrate this into the code. Could you perhaps suggest how and whethe ...
written 10.4 years ago by Jabez Wilson150
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Answer: A: Limma analyse factorial data with two-color arrays
... Thanks for you prompt reply, James. I'm familiar with you from your postings on the SAM mailing lists, so am honoured that you can reply to my query. Whilst I don't want to take bread out of honest statisticians mouths, I've been asked to analyse using limma an experiment that's already taken place ...
written 10.4 years ago by Jabez Wilson150
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Answer: A: Limma analyse factorial data with two-color arrays
... Sorry.... sent too soon. Dear all, I know that this question has been asked in a couple of forms, but I haven't noticed a full reply given. I'm hoping that someone will be able to give me the exact answer. I'm comparing stimulated cells vs unstimulated cells on each slide at two time points (4 hrs ...
written 10.4 years ago by Jabez Wilson150
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Limma analyse factorial data with two-color arrays
... Dear all, I know that this question has been asked in a couple of forms, but I haven't noticed a full reply given. I'm hoping that someone will be able to give me the exact answer. I'm comparing stimulated cells vs unstimulated cells on each slide at two time points. Suppose there are three samples ...
written 10.4 years ago by Jabez Wilson150

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Popular Question 7.7 years ago, created a question with more than 1,000 views. For limma data frame subsetting problem

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