User: kieranrcampbell

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Posts by kieranrcampbell

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Comment: C: Disagreement between TMM (edgeR) and RLE (DESeq) normalisation for single-cell d
... Hi Aaron, Thanks very much for this. Entirely makes sense that if we use endogenous genes then we'll disproportionately change the (presumably constant) ERCCs. I think I'm still somewhat confused as there seems to be conflicting advice as to whether ERCCs are stable enough for valid estimates, and ...
written 18 months ago by kieranrcampbell10
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Disagreement between TMM (edgeR) and RLE (DESeq) normalisation for single-cell data
... Hi all, I have an (admittedly poor quality) single-cell RNA-seq dataset. I was en-route to performing the "highly variable gene selection" from http://www.nature.com/nmeth/journal/v10/n11/extref/nmeth.2645-S2.pdf, and looked at the difference of the TMM normalisation factors from edgeR and RLE from ...
rnaseq normalization edger deseq2 single cell written 18 months ago by kieranrcampbell10 • updated 18 months ago by Aaron Lun18k
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Comment: C: Justification for collapsing technical replicates in DESeq2
... Okay I think I was just confused by terms here and thought technical replicate and batch (ie independent library prep) were equivalent. Entirely makes sense that if you do different sequencing runs of the same library then just to sum the counts. ...
written 19 months ago by kieranrcampbell10
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Comment: C: Justification for collapsing technical replicates in DESeq2
... Hi Mike, Thanks for your answer. The last part relates to an RNA-seq dataset I'm currently working on where batch effect dominates (ie technical replicate variability is large, sadly explains ~80% variance in the data...). So the follow-up questions would be (1) what's the best practice for dealing ...
written 19 months ago by kieranrcampbell10
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Justification for collapsing technical replicates in DESeq2
... Hi all, Can someone enlighten me as to the justification for summing counts across technical replicates in DESeq2, especially with respect to the collapseReplicates() function? I would have thought that statistically the correct thing to do would be to build a column into the design matrix to acco ...
rnaseq deseq2 differential expression replicate written 19 months ago by kieranrcampbell10 • updated 19 months ago by Michael Love16k

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