User: hanna.sinkko

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hanna.sinkko10
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Finland
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4 years, 4 months ago
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4 years, 4 months ago
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h***********@helsinki.fi

Posts by hanna.sinkko

<prev • 3 results • page 1 of 1 • next >
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Answer: A: question about variance stabilizing transformation and size factors in DESeq2
... Hi I upgraded Bioconductor and DESeq2 but I got installed only the version 1.6.3. I think I need to update my R to the current version as well. However, I tried to normalize with DESeq2 1.6.3. and did not succeed to produce correct size factors. Interestingly, I noticed that DESeq2 has produced siz ...
written 4.3 years ago by hanna.sinkko10
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Answer: A: question about variance stabilizing transformation and size factors in DESeq2
... And here is the sessionInfo() sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] C attached base packages: [1] parallel  stats     graphics  grDevices utils     datasets  methods   base      other attached packages: [1] phyloseq_1.8.2            D ...
written 4.3 years ago by hanna.sinkko10
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question about variance stabilizing transformation and size factors in DESeq2
... I'm very thankful if anybody have time to help!  Is the estimation of size factors included in VST normalization? I assumed according DESeq2 manual that VST normalization includes the estimation of size factors but I noticed that the size factor after VST normalization was same for all libraries, t ...
deseq2 written 4.3 years ago by hanna.sinkko10

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