## User: glmazzo

glmazzo0
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#### Posts by glmazzo

<prev • 9 results • page 1 of 1 • next >
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... HI liushang, I am having the same issue. Any luck with it? Thank you. Gianluca ...
written 9 weeks ago by glmazzo0
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... HI liushang, I am having the same issue. Any luck with it? Thank you. Gianluca ...
written 9 weeks ago by glmazzo0
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... 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 2.6 years ago by glmazzo0
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... 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 2.6 years ago by glmazzo0
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... 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 ...
written 2.6 years ago by glmazzo0 • updated 2.6 years ago by Michael Love26k
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... 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 2.6 years ago by glmazzo0
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... Dear Mike, thank you for your help. I run the code as you suggested. cqnOffset <- cqnObject$glm.offset cqnNormFactors <- exp(cqnOffset) normFactors<- cqnNormFactors / exp(rowMeans(log(cqnNormFactors))) normalizationFactors(dds)=normFactors Anyway when I tested the normalized count ... written 2.6 years ago by glmazzo0 2 answers 1.0k views 2 answers ... Dear Mike and Robin, as Robin pointed out, I am still a bit confused about how to include the normalizationFactors matrix from cqn into DESeq2. I believe that the right way (this is the only way I see an improvement in the GC and length bias) should be: cqnOffset <- cqnObject$glm.offset  cqnN ...
written 2.6 years ago by glmazzo0
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