User: cahidora

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cahidora40
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Posts by cahidora

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Comment: C: Differential expression analysis starting from TPM data
... There is no one better than you to answer this question (for good or bad). I appreciate very much your recommendations. ...
written 2.3 years ago by cahidora40
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Comment: C: Differential expression analysis starting from TPM data
... Gordon suggests this: logCPM <- cpm(dge, log=TRUE, prior.count=3) fit <- lmFit(logCPM, design) fit <- eBayes(fit, trend=TRUE) topTable(fit, coef=ncol(design)) that is why I was trying to create the variable "design". In "dge" i am using the log2FC values, is that right? ...
written 2.3 years ago by cahidora40
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Comment: C: Differential expression analysis starting from TPM data
... Here here I read that Gordon Smyth does not recommend to  use normalised values in DESeq, DESeq2 and edgeR. So I calculated the average of every group (C and D) and then I calculated the log2FC. With those log2FC values, I tried to follow the limma-trend pipeline described in the limma documentation ...
written 2.3 years ago by cahidora40
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Differential expression analysis starting from TPM data
... Hello, I am new in this kind of analysis and I have a .csv file containing RNA-Seq data from different cell lines (with at least 3 replicates) normalised to TPM already, unfortunately I cannot access to the raw counts files.      Symbol       ID              C1    C2     C3      D1      D2         ...
R tpm written 2.3 years ago by cahidora40 • updated 2.3 years ago by Gordon Smyth39k

Latest awards to cahidora

Great Question 2.3 years ago, created a question with more than 5,000 views. For Differential expression analysis starting from TPM data
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Differential expression analysis starting from TPM data

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