User: chwhite

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chwhite0
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Posts by chwhite

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Comment: C: EdgeR. Analysis with pairing across condition and treatment. Design Matrix
... Will do.  Thanks. ...
written 4.8 years ago by chwhite0
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Comment: C: EdgeR. Analysis with pairing across condition and treatment. Design Matrix
... Will do.  One last thing.  I noticed that when I use ~0+Treatment+Patient, it contains all of the Treatments but it is missing the first patient.  Since I'm not using the subtraction design, do I need all Patients in this.  A work around I played with was to add in a 0 level when generating the Pati ...
written 4.8 years ago by chwhite0
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Comment: C: EdgeR. Analysis with pairing across condition and treatment. Design Matrix
... Thanks, and answered above.  I had read the blocking effect but was unsure how to insert the Condition information into the design.  If I separated the two conditions, then I would use the following. design(~Patient+Treatment) I was also confused on how to set this up as in section 3.3.1 without t ...
written 4.9 years ago by chwhite0
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Comment: C: EdgeR. Analysis with pairing across condition and treatment. Design Matrix
... Thanks for the information.  I am interested in comparing the effect of the treatment (D vs. S, D vs. R, S vs. R) in both inf and uninf conditions.  I am also interested in the differences between the inf and uninf conditions under the effect of all 3 treatments.  The reasons it is a paired design ...
written 4.9 years ago by chwhite0
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EdgeR. Analysis with pairing across condition and treatment. Design Matrix
... I have the following experimental design and wanted to check the construction of the design matrix as well as a few other questions about setting it up.  Patient<-c("P1","P1","P1","P2","P2","P2","P3","P3","P3","P4","P4","P4","P1","P1","P1","P2","P2","P2","P3","P3","P3","P4","P4","P4") Condition ...
edger anova design matrix written 4.9 years ago by chwhite0 • updated 4.9 years ago by Gordon Smyth39k
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Comment: C: EdgeR User Guide. Analysis with multiple factors. Section 3.3.1
... Thanks for the info.  I will look into it.  ...
written 4.9 years ago by chwhite0
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EdgeR User Guide. Analysis with multiple factors. Section 3.3.1
... I am confused by something in the edgeR user guide in section 3.3.1.  The worked example indicates that each sample is obtained from independent subjects but the Sample name in the sample column seems to indicate that the Drug and Placebo samples are paired (i.e. Sample1, Sample2, etc.).  Is this e ...
edger anova written 4.9 years ago by chwhite0 • updated 4.9 years ago by Gordon Smyth39k

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Popular Question 4.8 years ago, created a question with more than 1,000 views. For EdgeR User Guide. Analysis with multiple factors. Section 3.3.1
Popular Question 4.8 years ago, created a question with more than 1,000 views. For EdgeR. Analysis with pairing across condition and treatment. Design Matrix

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