Bioconductor T-test

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EdgeR ANOVA t-test contrast

updated 7.4 years ago by Aaron Lun ★ 28k • written 7.4 years ago by Maiv • 0

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limma t-test

updated 7.2 years ago by James W. MacDonald 67k • written 7.2 years ago by Marek Gierlinski ▴ 30

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t-test GAGE package Kolmogorov-Smirnov test Gene-Set enrichment

8.4 years ago smt8n • 0

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deseq2 batch sva t-test design matrix

updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by Mozart ▴ 30

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Comment: How to annotate a limma Elist raw class object with an annotation file by James W. MacDonald 67k

Oh right. My bad. Good for you though, figuring out that it's ENTREZID, not ENTREZGENE. You did a good job of reading the error message in …

Comment: Differential Expression Genes as Independent Variables by James W. MacDonald 67k

Both true, so a poor suggestion on my part. I am also unclear as to how one would use a single observation (the gene expression measures)…

Answer: How to annotate a limma Elist raw class object with an annotation file by giulia.gentile • 0

Good afternoon, Thank you for your explanation and suggestion to overcome the issue by annotating directly from the genome-wide annotation…

Comment: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k

IIRC loading ~million cells into memory took about 3-5 minutes, but that was with a rather slow filesystem (HDD on a HPC), so YMMV dependin…

Comment: Differential Expression Genes as Independent Variables by Gordon Smyth 52k

Does not allow mixed models. And is for a different purpose to what your aims seem to be: it's purely for prediction rather than for testin…

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conumee with Infinium MethylationEPIC v2.0

A: How to bin a GRanges to small bins

C: How to bin a GRanges to small bins

A: deseq2 filter the low counts

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