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BiomaRt connection error: Could not connect to mysql database ensembl_mart_104
biomaRt connection sql
updated 3.5 years ago by ▴ 80 • written 3.5 years ago by ▴ 10
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MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI NCBI SQL AnnotationForge
updated 4.5 years ago by 67k • written 4.5 years ago by • 0
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Job: Full-time bioinformatics instructor position at Fred Hutch
R shell Python SQL Job
6.8 years ago ematsen ▴ 20
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Job: Harvard Medical School: Biomedical Data Scientist Postdoctoral Associate
biomedical informatics data science python SQL Job
8.8 years ago Doe, Aimee ▴ 40
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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 ▴ 880
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 ▴ 880
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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Answer: ANOVA like approach of edgeR
A: ANOVA-like test with edgeR
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
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