User: S.Bamopoulos

gravatar for S.Bamopoulos
S.Bamopoulos10
Reputation:
10
Status:
New User
Location:
Germany
Last seen:
9 months ago
Joined:
2 years ago
Email:
s******************@gmail.com

Posts by S.Bamopoulos

<prev • 8 results • page 1 of 1 • next >
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Comment: C: makeContrasts for comparing multiple levels of a factor variable to the referenc
... Thank you for the quick response!   ...
written 9 months ago by S.Bamopoulos10
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makeContrasts for comparing multiple levels of a factor variable to the reference level
... Hello all, I have a quick question regarding the makeContrasts function of the limma package, for which I couldn't find a clear answer online. I am running a differential expression pipeline and I want to explore the effect of 3 mutations, lets call them: mutA, mutB, mutC. I built a design matrix b ...
limma makecontrasts diffrential expression written 9 months ago by S.Bamopoulos10 • updated 9 months ago by Gordon Smyth37k
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Comment: C: Building a biologically meaningful design matrix for limma/voom in a large RNASe
... Thank you for taking the time to answer all my questions. I will take your suggestions into account and think about the best way to approach this issue Cheers Stefan ...
written 10 months ago by S.Bamopoulos10
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Comment: C: Building a biologically meaningful design matrix for limma/voom in a large RNASe
... Thanks a lot for the quick reply, it has improved my understanding of limma quite a bit. Just a quick follow-up: 1) I have some samples that don't have mutations in gene A, B or C but have other mutations with unknown effects and I don't want to use them as controls. What is the best way to include ...
written 10 months ago by S.Bamopoulos10
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Comment: C: Building a biologically meaningful design matrix for limma/voom in a large RNASe
... Hello Aaron, thank you for your answer, it is very detailed and insightful. I would greatly appreciate it, if you could clarify at least some of the points below: 1) I certainly understand why your suggestion of modelling the mutations as a factor is computationally efficient, but I am unsure as t ...
written 10 months ago by S.Bamopoulos10
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Building a biologically meaningful design matrix for limma/voom in a large RNASeq experiment
... Hello, I have a question regarding differential expression (DE) with limma/voom in an RNA-Seq experiment of ~250 samples. I already posted this question on Biostars and it was suggested that I also post here. I have 4 different point mutations that are mutually exclusive and I wish to identify DE ...
limma limma design matrix confounders limma-voom written 10 months ago by S.Bamopoulos10 • updated 10 months ago by Aaron Lun23k
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Comment: C: GOseq: count bias correction variations?
... Hello Gordon, I believe I understood Cristopher's question correctly, but I may be mistaken. I am using Salmon and from my understanding of the documentation the "effective length" given as an output accounts for at least some of the read count bias present in the data: "EffectiveLength — This is ...
written 2.0 years ago by S.Bamopoulos10
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Comment: A: GOseq: count bias correction variations?
... Hey all, I would also be really interested in an answer to this problem. Especially since in the voom paper it has been suggested that unequal library sizes lead to significantly different results. Additionally, new light-weight algorithms provide an "effective length" instead of the actual gene le ...
written 2.0 years ago by S.Bamopoulos10

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