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Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
updated 15 months ago by
ATpoint
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written 15 months ago by
kalavattam
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updated 15 months ago by
Michael Love
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written 15 months ago by
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2.7 years ago
mb1996
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2.8 years ago • updated 2.7 years ago
maria.soler
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updated 7 months ago by
Miguel
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written 3.2 years ago by
robert.chen
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Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
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Thank for your response. It is Illumina 450 K. I use this code
```{r }
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
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5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed):
```
limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
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0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
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4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
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