User: mouchkam

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mouchkam10
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10
Status:
New User
Location:
United States/Portland
Last seen:
2 years, 6 months ago
Joined:
2 years, 7 months ago
Email:
m*******@reed.edu

Posts by mouchkam

<prev • 3 results • page 1 of 1 • next >
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Comment: C: EdgeR Multifactorial design with batch effect-trouble with defining contrasts
... Thanks for the feedback Aaron.  All of the head samples cluster together (except for the sample C2H2, which is driving me crazy) and all of the body samples cluster together and far from the head samples in the MDS plot.  In addition, if you compare expression between heads and bodies, you get far m ...
written 2.6 years ago by mouchkam10
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Comment: C: EdgeR Multifactorial design with batch effect-trouble with defining contrasts
... Thank you so much Ryan, James and Aaron.  Your responses are very helpful and informative.  Just out of curiosity, is there any benefit to having an intercept design?   And if I may ask one more question regarding design, I'm wondering if it makes more sense to analyze my head and body datasets sep ...
written 2.6 years ago by mouchkam10
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EdgeR Multifactorial design with batch effect-trouble with defining contrasts
... Hello, I'm using EdgeR to identify differentially expressed transcripts from RNASeq data.  I have a fairly complicated experimental design with multiple time points, treatments, and tissue types.  In addition, because of limited amounts of experimental material, the replicates were collected at thr ...
edger design and contrast matrix multiple factor design multiple comparisons written 2.6 years ago by mouchkam10 • updated 2.6 years ago by James W. MacDonald45k

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