User: Moritz E. Beber

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10
Status:
New User
Location:
European Union
Last seen:
3 years, 8 months ago
Joined:
6 years, 5 months ago
Email:
m***********@gmail.com

Posts by Moritz E. Beber

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Comment: C: Effect size in non-standard linear model treatment experiment
... What would your recommendation then be to summarize that information? Simply record the maximum value of the F-statistic over all contrasts? ...
written 3.7 years ago by Moritz E. Beber10
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Comment: C: Effect size in non-standard linear model treatment experiment
... My exact code is at work but it goes something like this: I have a data frame that describes the expression levels. The experiments were measured at 3 time points after application of the drug and 4 different dosage levels. So you could construct it in the following way: data.frame( row.names ...
written 3.7 years ago by Moritz E. Beber10
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Effect size in non-standard linear model treatment experiment
... Dear all, I'm analyzing a large number of microarray treatment experiments. I have modeled the expression level as a dependent variable of the continuous independent variables time and dose as well as their interaction. As an R formula: ~ time + dose + time:dose Now I would like to estimate the ...
microarray limma effect size written 3.7 years ago by Moritz E. Beber10 • updated 3.7 years ago by Aaron Lun24k
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Comment: C: Design that evaluates response to continuous and categorical variables
... Fair point, I suppose. Thank you for your time and effort. ...
written 4.0 years ago by Moritz E. Beber10
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Comment: C: Design that evaluates response to continuous and categorical variables
... Thank you for your comments. As mentioned time and dose can be non-integer numbers. Time is in the range of hours to a maximum of 4 weeks. Doses vary widely and can be anywhere from a fraction to several thousand. The units are different per separate compound considered. The shown targets are for ...
written 4.0 years ago by Moritz E. Beber10
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Design that evaluates response to continuous and categorical variables
... Dear all, I'm trying to use limma in order to analyze a large number of Affymetrix microarrays. The experimental setup includes 2-3 replicates, 2-4 different time points and 1-5 different dosage levels. So a typical targets file could look like the following where the time and dose can be non-inte ...
limma design and contrast matrix limma design matrix design matrix written 4.0 years ago by Moritz E. Beber10 • updated 4.0 years ago by James W. MacDonald50k
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Comment: C: limma: Using log2 fold changes as input for a linear model fit
... The data are from treatment experiments that have a dose and time dependency, so that I just fit a linear model to the FC as a function of time and dose. However, the lack of variability and significance information of the FCs is a big concern to me, too, so I'll try to obtain the raw data, I suppos ...
written 4.1 years ago by Moritz E. Beber10
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limma: Using log2 fold changes as input for a linear model fit
... My data are log2 fold changes (FCs) between control and treatment usually coming from triple replicated affymetrix microarrays. I also have p-values for those data determined by t-test. As I currently have only those data available and not the replicates themselves, I wonder if it is sensible to use ...
limma logfc lmfit written 4.1 years ago by Moritz E. Beber10 • updated 4.1 years ago by Aaron Lun24k
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rhdf5 and factors
... Dear all, I sent a message to Bernd Fischer the maintainer of rhdf5 directly but got no response from him. My qualm lies with the writing and re- reading of factor vectors using rhdf5. In the current release they are simply written as integers and upon reading the HDF5 files the levels are obviousl ...
rhdf5 convert written 6.4 years ago by Moritz E. Beber10 • updated 6.4 years ago by Bernd Fischer540

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