User: cms72

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cms720
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Posts by cms72

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Comment: C: LogFC: how do you determine the cutoff for differentially expressed genes?
... And finally, one last question before my analysis is complete! edgeR's glmTreat is equivalent to Limma's treat, and both use Bayes method. However I noticed only Limma uses the adjust method "BH", which calculates an adj P-value. glmTreat does not provide any adj. p-value in its output. Would that ...
written 21 months ago by cms720
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Comment: C: LogFC: how do you determine the cutoff for differentially expressed genes?
... Hi Aaron, I'm trying to compare my logFC results to results that are in FC to see if I achieved the same gene expressions as they did, like if gene A is down-regulated in theirs, if its down-regulated in mine too.  I know the computation would be table$FC<- 2^(abs(table$logFC)). But then everyt ...
written 21 months ago by cms720
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Comment: C: LogFC: how do you determine the cutoff for differentially expressed genes?
... Hi Aaron,  Just a quick question, would the equivalent of topTreat in Limma be glmTreat in edgeR?  Thank you again in advance. ...
written 21 months ago by cms720
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Comment: C: LogFC: how do you determine the cutoff for differentially expressed genes?
... I see. Thank you again. Regarding voom, the reason why I never used it was because I have FPKM values and not read counts (I know its not ideal, but thats what I've got to work with. And yes, I have to use limma specifically and not cummerbund). My understanding is that voom normalises counts, wher ...
written 21 months ago by cms720
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Comment: C: LogFC: how do you determine the cutoff for differentially expressed genes?
... In addition to my earlier post. I was fiddling around with my results and found that if I added robust to both lmFit and Treat, it would result to more DEGs, with warnings saying small variances detected (I assume due to its robust regression): fit<-lmFit(Count, design, method = "robust") ..... ...
written 21 months ago by cms720
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Comment: C: LogFC: how do you determine the cutoff for differentially expressed genes?
... Hi Aaron, Thank you for your time and clarification. Your explanation makes sense. These are the steps I've undertaken.. I've followed the Limma manual, but I feel like my comprehension could be wrong. fit<-lmFit(Count, design, method = "robust") cont.matrix<-makeContrasts(Treatmentvscontrol ...
written 21 months ago by cms720
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LogFC: how do you determine the cutoff for differentially expressed genes?
... Hi, I was wondering if I could ask for confirmation regarding my understanding of logFC values. So I know when you get a negative logFC value, the gene is underexpressed, and when you get a positive logFC value, the gene is overexpressed. But is there a cutoff value? I read in an article that they ...
rnaseq limma R logfc differential gene expression written 21 months ago by cms720 • updated 21 months ago by Aaron Lun23k

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Popular Question 21 months ago, created a question with more than 1,000 views. For LogFC: how do you determine the cutoff for differentially expressed genes?

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