User: ea1402

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ea140220
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Posts by ea1402

<prev • 16 results • page 2 of 2 • next >
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GLM voom and link Function
... Hi all,   After reading about voom, limma and GLM, I highly get confused about link functions and voom. The log transformation of counts in limma-voom, is the logarithm serve as a link function in the GLM formalism or is it merely a scale transformation?  What is the most important reason for doin ...
limma voom written 4.3 years ago by ea140220 • updated 4.3 years ago by Aaron Lun25k
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Comment: C: Log fold change on Limma
... that makes sense and I am doing what you describe. In your case what does the lfc correspond in the treat () function,  (A+B)/(C+D)? Thanks ...
written 4.5 years ago by ea140220 • updated 4.5 years ago by Gordon Smyth39k
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Comment: C: Multiple Testing Correction
... Hi James, thanks for the reply for the limma analysis I am using the treat function. However, I have my own method of calculation p-values for the significance of each comparison. However, considering my data I would like to say a change is statistifically significant whether the fold change is abo ...
written 4.5 years ago by ea140220
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Comment: C: Log fold change on Limma
... Hi Ryan, Yes since I have three replicates I am testing (A+B)/3-(C+D)/3=0, what does the fold change represent in this case? ...
written 4.5 years ago by ea140220 • updated 4.5 years ago by Gordon Smyth39k
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Log fold change on Limma
... Hi, I am analyzing an RNA seq experiments using limma in which I have 4 different RNA species A,B,C,D and each has three replicates.  I am using the follwing (assuming data_counts is my count matrix) dge <- DGEList(counts=data_counts1,lib.size=libsizee) dge<-calcNormFactors(dge,lib.size=lib ...
limma multiple factor design written 4.5 years ago by ea140220 • updated 4.5 years ago by Steve Lianoglou12k
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Multiple Testing Correction
... Hi, I am running couple of different differential expression analysis on my data. I have a quick question that confuses me. Suppose I am using a lfc threshold of x, when correcting for multiple should I use only the genes that have a lfc greater than my lfc threshold or should I use all the genes ...
rnaseq limma moderated t-test written 4.5 years ago by ea140220

Latest awards to ea1402

Popular Question 3.1 years ago, created a question with more than 1,000 views. For Limma Camera error
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Log fold change on Limma

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