User: glmazzo

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Posts by glmazzo

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Comment: C: GC content and length bias correction with DESeq2 using cqn normalization factor
... Great! Thank you so much for your help. If I understood correctly, you suggest to perform the DE analysis using cqn to correct for between samples (GC content and length) bias. I know that the gene length and GC content bias within sample does not compromise DE results but that they affect the fun ...
written 7 months ago by glmazzo0
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Comment: C: GC content and length bias correction with DESeq2 using cqn normalization factor
... Dear Mike, Noiseq generates a plot for each sample for the GC content (plot showed in the post) and a plot for each sample for the length bias (plot not showed in my post) The plots look similar across the sample (both for GC content and length bias). I attached here the plots for other samples ( ...
written 7 months ago by glmazzo0
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GC content and length bias correction with DESeq2 using cqn normalization factor matrix
... Hi everybody, I am working with RNASeq data.  I am using DESeq2 and I would like to correct for the GC content and length bias using cqn. When I tested the normalized counts with NOISeq to test if the biases were corrected, I noticed that when I divided out the normalization factors by the geom ...
cqn noiseq deseq2 written 7 months ago by glmazzo0 • updated 7 months ago by Michael Love15k
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Comment: C: DESeq2 and CQN how to use offsets and get transformations?
... Dear Mike,  I attached three plots made with NOISeq to test for GC contenct bias, that I used to test the effect of the cqn correction. From NOISeq manual: “The GC content is divided in intervals (bins) containing 200 features. The middle point of each bin is depicted in X axis. For each bin, the ...
written 7 months ago by glmazzo0
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Comment: C: DESeq2 and CQN how to use offsets and get transformations?
... Dear Mike, thank you for your help. I run the code as you suggested. cqnOffset <- cqnObject$glm.offset cqnNormFactors <- exp(cqnOffset) normFactors<- cqnNormFactors / exp(rowMeans(log(cqnNormFactors))) normalizationFactors(dds)=normFactors   Anyway when I tested the normalized count ...
written 7 months ago by glmazzo0
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Comment: C: DESeq2 and CQN how to use offsets and get transformations?
... Dear Mike and Robin, as Robin pointed out, I am still a bit confused about how to include the normalizationFactors matrix from cqn into DESeq2. I believe that the right way (this is the only way I see an improvement in the GC and length bias) should be: cqnOffset <- cqnObject$glm.offset  cqnN ...
written 7 months ago by glmazzo0
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DESeq2 residuals log transformation input for WGCNA
... I am working with RNA seq data. I would like to compute the residuals with DESeq2 to remove confounding effect in the data before running WGCNA.   We computed the residuals by using  DESeq2 on our RNA Seq count matrix with this code: fitted.common.scale = t(t(assays(dds)[["mu"]])/sizeFactors(dds) ...
deseq2 wgcna residuals written 8 months ago by glmazzo0 • updated 8 months ago by Steve Lianoglou12k

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