User: dietahanson

gravatar for dietahanson
dietahanson30
Reputation:
30
Status:
New User
Location:
McGill University, Montreal, Canada
Last seen:
1 year, 4 months ago
Joined:
2 years, 1 month ago
Email:
d**********@gmail.com

Posts by dietahanson

<prev • 7 results • page 1 of 1 • next >
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Comment: C: edgeR cpm filter with >1 factor
... Ok, I see what you're saying, I guess I was just misinterpreting that part of the documentation.   Thanks! ...
written 22 months ago by dietahanson30
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Answer: A: edgeR cpm filter with >1 factor
... Thanks very much for your answer!   But when you say "we mean expressed in all the samples of that condition", the code in section 2.6 of the documentation would not necessarily achieve this, at least as I read it. There are two conditions, one of which has three replicates and one of which has tw ...
written 22 months ago by dietahanson30
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edgeR cpm filter with >1 factor
... I have two questions regarding the cpm filter suggested for edgeR: 1. I am confused by the statement from the documentation "As a rule of thumb, genes are kept if they are expressed in at least one condition.". If this were the case, in the example given in section 2.6, wouldn't the filter be simp ...
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Comment: C: Different results in edgeR using simple vs GLM
... Thanks for your answer, I think I understand now what the second coefficient is testing (though the name is misleading!). Those three contrasts then are exactly what I'm looking for--glad to know I can just use my original design matrix. Thanks again! ...
written 2.1 years ago by dietahanson30
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Answer: A: Different results in edgeR using simple vs GLM
... Thanks everyone for your responses (I didn't realize until now that the conversation had continued after James' response, so sorry for the late reply--I really appreciate your answers!). I should clarify exactly what it is I am trying to accomplish by fitting the model that I did. I am looking for ...
written 2.1 years ago by dietahanson30
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Answer: A: Different results in edgeR using simple vs GLM
... That makes sense--I didn't even think of the fact of increasing the degrees of freedom.     Thanks a lot for your help!     ...
written 2.1 years ago by dietahanson30
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Different results in edgeR using simple vs GLM
... Hi there,     I'm using edgeR version 3.10.2 to analyze my RNAseq data. I have a design in which there are two factors (habitat and watershed) with two levels in each factor. I have 3 replicates for each of the four groups, to make 12 samples total. I am also interested in the interaction between ...
rnaseq edger glm written 2.1 years ago by dietahanson30

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