User: b.nota

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b.nota290
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Netherlands
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3 days ago
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3 years, 2 months ago
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Posts by b.nota

<prev • 125 results • page 1 of 13 • next >
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Comment: C: Limma model for paired and pool together
... The pool is made of 3 other donors, so this will work for me! Thanks both. ...
written 4 days ago by b.nota290
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Limma model for paired and pool together
... I would like to use limma (voom or trend) for my RNAseq analysis, and I am wondering how to correctly model my data. I have 2 different cells (hi and lo) from 2 donors, so I want to use a paired design. However, there is also a pool of more donors (hi and lo). How can I include this correctly in my ...
rnaseq limma design written 4 days ago by b.nota290 • updated 4 days ago by Ryan C. Thompson6.5k
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Comment: C: edgeR cpm() function with and without log2
... Thanks for the link (with Gordon's answer) and explanation. So important is the fact that e.g., 1 fold change stays 1 fold change with scaling. ...
written 5 weeks ago by b.nota290
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edgeR cpm() function with and without log2
... Hello, I have a question about the cpm function from edgeR. When I use this function with log = T, I get different results from when I use it without followed by log2 transformation afterwards. What did I miss here? Edit: Has this to do with the scaling of the prior count? If yes, what is the bene ...
edger cpm written 5 weeks ago by b.nota290 • updated 5 weeks ago by Aaron Lun19k
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Comment: C: Limma Voom produces many identical adjusted p-values
... Perry, thanks for explanation and link to earlier posts! ...
written 3 months ago by b.nota290
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Comment: C: Limma Voom produces many identical adjusted p-values
... When I put them in a plot, it seems kind of weird, I got complaints from my fellow researchers. They should be adjusted p-values, right? That is something else than just false discovery rates. ...
written 3 months ago by b.nota290
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Comment: C: Limma Voom produces many identical adjusted p-values
... Thanks Axel, so can I just use these adjusted p-values? Or can I fix it? ...
written 3 months ago by b.nota290
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Limma Voom produces many identical adjusted p-values
... I have used limma voom for a simple RNAseq experiment (with two conditions), and in the end many genes have exactly the same adjusted p-value. I was wondering if this is an artifact? Or an error in the program? Or any other explanation?   In a nutshell here the essential code. dge <- DGEList( ...
adjusted pvalue limma voom written 3 months ago by b.nota290 • updated 3 months ago by Gordon Smyth33k
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Comment: C: edgeR design between and within subjects
... Thanks for your explanation. So for the last part, which is only possible as indirect comparison (MUT.TEM vs WT.TEM). What will be the meaning of the fold changes in the topTags results? So I understand that the patient blocking does not make sense for such comparison (since WT patient 1 is not the ...
written 8 months ago by b.nota290
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edgeR design between and within subjects
... Hello, I am trying to do edgeR analysis, such as described in 3.5 of the manual. My experiment is very alike, but I don't exactly understand how to get all the contrasts of my interests. Here some code: > data.frame(Genotype, Cell, Patient) Genotype Cell Patient 1 WT TCM 1 2 ...
edger design and contrast matrix written 8 months ago by b.nota290 • updated 8 months ago by Aaron Lun19k

Latest awards to b.nota

Scholar 13 months ago, created an answer that has been accepted. For A: warning in R
Centurion 14 months ago, created 100 posts.
Supporter 24 months ago, voted at least 25 times.
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: warning in R
Scholar 2.0 years ago, created an answer that has been accepted. For A: warning in R
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: warning in R
Scholar 2.8 years ago, created an answer that has been accepted. For A: warning in R

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