User: FAVI

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FAVI0
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Posts by FAVI

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Answer: A: [limma - v. 17 June 2014] Log2 or not to log2 the data? (Agilent single-channel
... Problem found. It seems like, at least in the version I have been using (limma_3.22.1), the function "normalizeBetweenArrays()"  uses raw/background corrected intensities as input and, internally, it automatically (log2)transforms the data (at the same time it performs the normalization (i.e. quant ...
written 4.1 years ago by FAVI0
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Comment: A: [limma - v. 17 June 2014] Log2 or not to log2 the data? (Agilent single-channel
... Moreover, I noticed that output from "topTable(fit2)" [After having defined fit1 <- lmFit(y, design) / fit2 = contrasts.fit(fit1, contrastMatrix) / fit2 = eBayes(fit2)] is totally different: Without log2-transforming: Highest logFC ~ 1.540, lowest logFC ~ -2.586 With log2-transformed data: High ...
written 4.1 years ago by FAVI0
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[limma - v. 17 June 2014] Log2 or not to log2 the data? (Agilent single-channel microarray data)
...   Hi all, I'm working with Agilent single-channel microarray data. However, it's not clear to me whether raw data should be log2 transformed or not (or if it's intrinsically done "behind the scenes"): 1) In some places (http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_mic ...
limma logfc normalizebetweenarrays() written 4.1 years ago by FAVI0

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