User: Michael Breen

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Michael Breen350
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Posts by Michael Breen

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Comment: C: Combat Continuous
... Thanks for the response and nice discussion. To summarize, we have deconvolved blood gene expression from 4 time points into cell-type frequencies. After, we are interested in taking into account differences in cell-type frequencies in our linear model for DE testing. In this example it is tricky t ...
written 3.5 years ago by Michael Breen350
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Comment: C: Combat Continuous
... Peter, I considered re-titling this post however we can leave it as is. On Mon, May 12, 2014 at 10:48 PM, Peter Langfelder < peter.langfelder@gmail.com> wrote: > Hi Michael, > > On Mon, May 12, 2014 at 1:23 PM, Michael Breen > wrote: > > > As far as deconvoultion anal ...
written 3.5 years ago by Michael Breen350
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Comment: C: Combat Continuous
... Peter, Thanks for the clarification of Combat continous variables vs. factors. That is the information I was missing. As far as deconvoultion analysis, we currenlty are using Zhong et al. (2013) DSA method using HaemAtlas to provide a signature matrix (or cell-type marker list). The method estimat ...
written 3.5 years ago by Michael Breen350
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Answer: A: Combat Continuous
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written 3.5 years ago by Michael Breen350
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Combat Continuous
... Hi all, I have time course gene-expression from blood at 4 different time points. During the last two time points we see an increase in various different cell-type frequencies. We are interested in correcting our gene expression matrix with numerous continuous variables, that is estimated cell-type ...
written 3.5 years ago by Michael Breen350
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Comment: C: Voom Normalization and negative numbers
... Thanks Wade, Is there not a difference when interpreting a calculated negative ∆ between two relative measures of expression and a calculated negative log cpm for just one measure? I also believe that differential expression or correlation analysis would not be harmed by this. But I thought to g ...
written 3.6 years ago by Michael Breen350
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Comment: C: Voom Normalization and negative numbers
... Thank you for the explanation. It was in fact quite obvious. However, does there arise conceptual problems with comprehending negative expression values? We know, the cpm is somewhere between 0-1, but does the log derivative of these numbers cause any down-stream problems? Differential expression o ...
written 3.6 years ago by Michael Breen350
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Voom Normalization and negative numbers
... Hi all, We are applying Voom normalization to RNA-Seq Counts with the following code: library(edgeR) count <- read.delim("Counts.txt", check.names=FALSE, stringsAsFactors=FALSE) targets <- read.delim("Targets.txt", check.names=FALSE, stringsAsFactors=FALSE) #filter y <- DGEList(counts=r ...
normalization written 3.6 years ago by Michael Breen350 • updated 3.6 years ago by Davis, Wade340
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Comment: C: ANCOVA microarray time-course continuous & categorical variables / Limma extensi
... Hi all, Recently, there has been considerable interest in these types of studies, i.e. those outlined in section 8.7 Multi-level Experiments (in the limma manual) while including continuous variables that may have overall effects on gene-expression outcomes. Not only is it informative to correlate ...
written 4.1 years ago by Michael Breen350
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Comment: C: ANCOVA microarray time-course continuous & categorical variables / Limma extensi
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written 4.1 years ago by Michael Breen350

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Popular Question 3.5 years ago, created a question with more than 1,000 views. For Voom Normalization and negative numbers

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