User: Hickman, R.J. Richard

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Posts by Hickman, R.J. Richard

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Comment: C: DESeq2 test over all timepoints?
... Hi Mike, That appears to have worked- thanks! Richard ________________________________ From: Michael Love [michaelisaiahlove@gmail.com] Sent: 12 February 2014 14:53 To: Hickman, R.J. (Richard) Cc: bioconductor@r-project.org Subject: Re: [BioC] DESeq2 test over all timepoints? Hi Richard, Can ...
written 3.8 years ago by Hickman, R.J. Richard50
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DESeq2 test over all timepoints?
... Dear Mike (and other DESeq2 developers/users), I came across this thread regarding the use of the GLM functions in DESeq2 with respect to time series. However, if I try and perform the analysis you describe then I get an error when estimating the dispersions? do you know what is the cause and/or wh ...
edger deseq deseq2 written 3.8 years ago by Hickman, R.J. Richard50 • updated 3.8 years ago by Michael Love14k
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DESeq Variance Stabilizing Transformation (now with non-embedded images)
... Dear Wolfgang and Michael, Thank you both for your comments. I applied the rlog transformation to our data and when I plot the per- gene standard deviation against the rank of the mean (see attached figure DESeq_count_transformations.png), it appears to perform better than the other two transforma ...
normalization clustering deseq deseq2 written 4.5 years ago by Hickman, R.J. Richard50 • updated 4.5 years ago by Michael Love14k
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Comment: C: DESeq Variance Stabilizing Transformation
... Hi Michael, For the plots attached to the previous message I used the following code: dds <- estimateSizeFactors(dds) dds <- estimateDispersions(dds) vsd <- varianceStabilizingTransformation(dds) I attach a new plot "timeseriesBlindVST.png" which was generated using the "blind" method: ...
written 4.5 years ago by Hickman, R.J. Richard50
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DESeq Variance Stabilizing Transformation
... Dear All, I am looking for some feedback regarding the use of the variance- stabilization (VST) methods found in the DESeq2 package. For me, the purpose for applying this transformation is to be able to generate moderated fold changes for clustering of genes (not samples as described in the DESeq v ...
clustering deseq deseq2 written 4.5 years ago by Hickman, R.J. Richard50 • updated 4.5 years ago by Michael Love14k

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Popular Question 3.8 years ago, created a question with more than 1,000 views. For DESeq2 test over all timepoints?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For DESeq Variance Stabilizing Transformation

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