User: Heather Estrella

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4 years, 6 months ago
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Posts by Heather Estrella

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What RNA-Seq expression estimates to use for plotting to show voom/limma Differential expression
... HI Dr. Smyth, I am trying to find the appropriate mRNA expression level estimates to use for generating plots that demonstrate the differential expression statistics calculated from voom/limma. What do you recommend? FPKM plots don't always agree with my voom/limma results. For example, if the dif ...
visualization graph limma written 4.5 years ago by Heather Estrella30 • updated 4.5 years ago by Gordon Smyth34k
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Voom and removing batch effect
... Hi, I have a miRNA-Seq dataset with clear batch effect that I'm trying to correct for in order to run differential expression using voom/limma. Based on the Limma User Guide, this can be done by adding batch as a confounding factor to the design matrix used by voom and limma fit. However, when I ru ...
normalization limma written 4.6 years ago by Heather Estrella30 • updated 4.6 years ago by Ryan C. Thompson6.8k
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Voom and CQN input
... This is in regards to a previous post by Dr. Gordon Smyth from June, 2012. https://stat.ethz.ch/pipermail/bioconductor/2012-June/045950.html In the previous post, Dr. Smyth stated: "voom() isn't currently setup to accept the normalization matrix from cqn, but it will be down the track." Does anyon ...
normalization limma cqn written 4.7 years ago by Heather Estrella30 • updated 4.7 years ago by Gordon Smyth34k

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Popular Question 4.5 years ago, created a question with more than 1,000 views. For Voom and removing batch effect

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