## User: Michael Breen

Michael Breen350
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#### Posts by Michael Breen

<prev • 34 results • page 1 of 4 • next >
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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 4.4 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 4.4 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 4.4 years ago by Michael Breen350
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written 4.4 years ago by Michael Breen350
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... 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 4.4 years ago by Michael Breen350
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... Thanks Wade, Is there not a difference when interpreting a calculated negative â 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 4.5 years ago by Michael Breen350
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... 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 4.5 years ago by Michael Breen350
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... 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 ...
written 4.5 years ago by Michael Breen350 • updated 4.5 years ago by Davis, Wade340
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... 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 4.9 years ago by Michael Breen350
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... I have done this in the past, although I did not have much faith in it, maybe because of the way I create the design matrix. For example I do it this way: Treat <- factor(paste(targets$Condition,targets$Time,sep=".")) design <- model.matrix(~0+Treat) colnames(design) <- levels(Treat) coln ...
written 4.9 years ago by Michael Breen350

#### Latest awards to Michael Breen

Popular Question 4.4 years ago, created a question with more than 1,000 views. For Voom Normalization and negative numbers

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