User: Magda Price

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Magda Price60
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Posts by Magda Price

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Paired samples and interactions models with bumphunter?
... Hi David - I'm looking to apply bumphunter in a similar way to what you have outlined. Have you made any progress? Thanks, Magda ...
written 2.6 years ago by Magda Price60
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ComBat: 2 adjustment variables & continuous adjustment variables
... Johnson, William Evan writes: > > Hey Magda, > > The two-step method is still a reasonable approach. It has worked well for me in multiple situations. I do > have a beta version of a ComBat version that will handle two batch variables at the same time. It works well > in theory-- ...
go category sva written 5.2 years ago by Magda Price60
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Comment: C: ComBat: 3 adjustment variables & continuous adjustment variables
... Unfortunately that doesn't work. Only one batch variable is allowed. Thanks for your suggestion though. On Wed, Mar 19, 2014 at 6:58 AM, James W. MacDonald wrote: > Hi Magda, > > I'm not sure you need to do things sequentially like that. From what I can > tell, you should just be ab ...
written 5.2 years ago by Magda Price60
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Comment: C: ComBat: 3 adjustment variables & continuous adjustment variables
... Hi Jim, Re numCovs - what you've stated was how I interpreted the use as well, which is why I didn't think it would helpful. As usual with these types of human disease datasets, the study design is not ideal, and more complicated than I initially let on! The 180 samples are a combination of 3 phen ...
written 5.2 years ago by Magda Price60
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Comment: C: ComBat: 3 adjustment variables & continuous adjustment variables
... Hi Jim, I have several different "batch" variables - one for example is the chip that each sample was run on (there are 24 of these) and I think chip batch should definitely be treated as a factor. Another "batch" variable I would like to adjust for is the position the sample was run on the chip (t ...
written 5.2 years ago by Magda Price60
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Comment: C: ComBat: 3 adjustment variables & continuous adjustment variables
... Hi Steve, Thanks for your advice. I do know that I'm using an old version of R (one of the packages I'm using requires it) however, the options you mention from sva are in fact available in the older version as well, but it wasn't clear to me how to use them. I've copied the usage and argument inf ...
written 5.2 years ago by Magda Price60
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ComBat: 2 adjustment variables & continuous adjustment variables
... Hi! I'm writing with a few questions about applying ComBat (sva package) to a set of ~50 samples run on the the Illumina Infinium HumanMethylation450 BeadChip array (~450,000 DNA methylation data points). There is a large amount of variation in my data due to both the batch the samples were run in ...
go category sva written 5.3 years ago by Magda Price60

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Popular Question 2.6 years ago, created a question with more than 1,000 views. For ComBat: 2 adjustment variables & continuous adjustment variables

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