User: Matthew Hannah

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Posts by Matthew Hannah

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double violation of normalization assumptions?
... >I would never normalize within treatment, as the normalization could >cause the apparent differential expression. > >In the absence of any suitable between array method, I would use >MAS5.0. Of course, the MM binding could also be affected if the >virus affects RNAs that bind to ...
microarray normalization probe limma gcrma written 13.2 years ago by Matthew Hannah940
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Answer: A: Biological replication (was RNA degradation problem)
... This is interesting and there are certainly contrasting views. It is also certainly not a bioC issue but is of interest. At the risk of dragging it on I don't think this statement should be left without the comments below. > -----Original Message----- > From: fhong at salk.edu [mailto:fhong a ...
written 13.2 years ago by Matthew Hannah940
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Answer: A: Biological replication (was RNA degradation problem)
... Lot of discussion here. A couple of points to make, mainly looking at the practical side. Perfectly reproducible growth conditions are almost non-existance. Climate controls are slightly influenced by the seasons, water status and light conditions depend on position (edge effects) and the presence ...
written 13.2 years ago by Matthew Hannah940
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Answer: A: Biological replication (was RNA degradation problem)
... > > The question of what is appropriate biological replication is > a tough one. The objective is to obtain results that are > valid in the population of interest, which usually is not > plants grown in a single batch in the green house. But how > much variability should we induc ...
written 13.2 years ago by Matthew Hannah940
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Answer: A: RNA degradation problem
... ________________________________ From: fhong@salk.edu [mailto:fhong@salk.edu] Sent: Thu 19/01/2006 21:27 To: Matthew Hannah Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] RNA degradation problem Hi Matthew, Thank you very much for your help. > >It's amazing how many >> ...
written 13.2 years ago by Matthew Hannah940
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RNA degradation problem
... Fangxin, Yes it looks like the data is less than ideal. The last chip certainly looks dubious and should probably be repeated. I would definetely check with the experimenter how the samples were harvested and process and CONFIRM that they are true biological replicates. It's amazing how many lab pl ...
normalization affy limma affyplm process written 13.2 years ago by Matthew Hannah940 • updated 13.2 years ago by Fangxin Hong810
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PLIER affinities redux
... Jeremy, I got distracted whilst still in draft and in the meantime Jim has responded. Anyway to add - I pasted your code into my fresh BioC install and it doesn't work with the ATH1121501 array either, it's inherent in the justPlier code. Looking at justPlier code shows that it returns a matrix of ...
ath1121501 cdf probe biobase affy plier written 13.4 years ago by Matthew Hannah940
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permutation/resampling FDR correction
... Hi, Rather than use the linear step-up FDR procedure I'd like to use a permutation method to correct p-values from limma. I use linear regression of 8 groups with 3 replicates against a numerical measure for the eight groups. ie: x <- c(1,1,1,3,3,3,6,6,6,4,4,4,8,8,8,7,7,7,5.5,5.5,5.5,6,6,6) des ...
regression limma written 13.7 years ago by Matthew Hannah940
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Answer: A: no BioConductor posting guide
... Good idea, couple of minor suggestions. I'd change 1 or 3 this to something along these lines to stress that all packages can be browsed for functions, their definitions and other package documentation using the html help. This is useful even if you don't know exactly what a function is or to get a ...
written 13.9 years ago by Matthew Hannah940
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Wilcoxon test [was loged data or not loged previous to use normalize.quantile]
... >Not forgetting that the two-sample t-test performs fine under the same circumstances (large >balanced samples), even for non-normal distributions and unequal variances. > >Regards >Gordon Does anyone by any chance have a few references for this point, particularly for non-normal dis ...
written 14.0 years ago by Matthew Hannah940 • updated 13.9 years ago by A.J. Rossini210

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Popular Question 13.2 years ago, created a question with more than 1,000 views. For Selecting p-value cutoffs for differential expression

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