User: ilovesuperheroes1993

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Posts by ilovesuperheroes1993

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Comment: C: Majority upregulated genes in edgeR
... Thanks Aaron for your suggestions. ...
written 12 weeks ago by ilovesuperheroes19930
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Comment: C: Majority upregulated genes in edgeR
... What I meant was that from the results, out of all the genes with FDR < 0.05, majority genes had a negative value of log(fc), which in this case means upregulated in disease. Very few had positive values of log(fc). (Downregulated) I have provided the number of total differential genes, and the ...
written 12 weeks ago by ilovesuperheroes19930
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Majority upregulated genes in edgeR
... Hi, I am doing a paired analysis between 24 pairs of Normal and Diseased samples, using edgeR. I take the entries with FDR < 0.05. Out of a total of around 57700 genes (including the multiple isoforms), I have obtained around 11500 genes within my selected FDR. However, among these, I find tha ...
edger differential expression genes fold change written 12 weeks ago by ilovesuperheroes19930 • updated 12 weeks ago by Aaron Lun24k
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Dependence of FDR and P-values on sample size
... Hi, I am doing a differential expression analysis of small RNA using edgeR. I have 4 normal and 4 diseased samples, all samples are paired. Now, I have very little knowledge of statistics so I would appreciate clarification on the following: When I do the analysis without any per-filtering of lo ...
edger fdr p-value differential analysis benjamini-hochberg written 6 months ago by ilovesuperheroes19930 • updated 6 months ago by Aaron Lun24k
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Differential Expression Analysis in edgeR using Anova
... Hi, I have 5 samples, namely the following: (1) Not transfected, untreated (2) Transfected but untreated (3) Transfected, treated, analyzed after 5 mins (4) Transfected, treated, analyzed after 60 mins (5) Transfected, treated, analyzed after 4 hrs [By transfected I mean a particu ...
edger anova dispersion gene expression written 8 months ago by ilovesuperheroes19930 • updated 11 weeks ago by onlychainsaw20190
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Comment: C: MDS Plot help in edgeR
... Thank you for your reply. I originally have used Method 1. But recently I saw a couple of pages where someone had suggested to use method 2, i.e. doing the MDS plot with the normalized counts. Could you please explain me why the second method is wrong, how the two methods are differing?   ...
written 8 months ago by ilovesuperheroes19930
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MDS Plot help in edgeR
... I am doing a differential genes analysis between 24 pairs of paired samples, normal vs diseased. I want to generate an MDS Plot to check if my normal and diseased samples are being clustered well. I am running edgeR for the analysis. Could anyone tell me the difference between the 2 methods given b ...
edger differential gene expression mds mdsplot plotmds written 8 months ago by ilovesuperheroes19930 • updated 8 months ago by Gordon Smyth38k
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Comment: C: EdgeR filtering, gene expression, cpm cutoff
... Thank you. Yes I think I had misread it. I've pasted the section of the manual below: > y$samples group lib.size norm.factors Sample1 1 10880519 1 Sample2 1 9314747 1 Sample3 1 11959792 1 Sample4 2 7460595 1 Sample5 2 6714958 1 We filter out lowly expressed genes using the following commands: &g ...
written 13 months ago by ilovesuperheroes19930
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Comment: C: EdgeR filtering, gene expression, cpm cutoff
... Yes, I have gone through that. Section 2.6 allows me to keep genes but a minimum no of samples in each group must have cpm above cutoff. I want to remove that restriction and apply that cutoff to a minimum of  ANY 4 samples. Let's say my cpm values for a gene are : Sample 1 Group 1--cpm 7 Sample ...
written 13 months ago by ilovesuperheroes19930
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EdgeR filtering, gene expression, cpm cutoff
... I am running a DE analysis on edgeR. I have 8 biological replicates, in groups of 2 (1 normal and 1 diseased) What I want to do is keep those genes, for which the cpm is above 4 in at least 4 of the samples (of total 8), irrespective of the group. Could anyone provide me with the necessary code? ...
edger tutorial written 13 months ago by ilovesuperheroes19930 • updated 13 months ago by Hotz, Hans-Rudolf400

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