Showing : phenoData • reset
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Made a pDATA manually for HTqPCR procedure
HTqPCR phenoData esetVis pData
3.1 years ago Marcelo Laia ▴ 450
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ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools ReadAffy Biobase phenoData affy
updated 3.9 years ago by 67k • written 3.9 years ago by • 0
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Sample grouping (phenoData) and visualization in R package- HtqPCR
HtqPCR grouping visualization R phenoData
5.3 years ago mohammedtoufiq91 ▴ 10
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Loading FCS files
FCS flow cytometry bioconductor phenoData Loading Data
updated 7.9 years ago by ▴ 350 • written 7.9 years ago by • 0
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Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k
I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…
Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 870
If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …
Comment: ANOVA like approach of edgeR by SamGG ▴ 350
Simply remove the cell type from the model. design <- model.matrix(~targets$Status)
Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 870
You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…
Answer: Identical samples after deseq2 batch effect removal by maripane • 0
Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…
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