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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
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Trying to use enrichGO
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Error for AnnotationForge makeOrgPackageFromNCBI function
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2 days ago • updated just now Gayatri • 0
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minfi::read.metharray.exp
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DESeq2 - dispersion estimation when there is none
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updated 18 hours ago by 41k • written 1 day ago by • 0
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DESeq2 output used for PCA plot on R studio
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updated just now by ★ 4.0k • written 16 hours ago by • 0
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get BM error
ensembldb
1 hour ago Fara • 0
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2
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How to retrieve gene ontology GO class from gene list?
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10 hours ago • updated 1 hour ago bandconductor • 0
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Citation for edgeR user guide
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
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updated 6 hours ago by 41k • written 13 hours ago by ▴ 40
0
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Opposite sign of LFC in count plots of DEGs (DESeq2)
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14 minutes ago winwater0928 • 0
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Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by Gayatri • 0
What I meant is even after deleting the NCBI.sqlite file, and re-running the script, an empty NCBI.sqlite file (0 kb) is created which is c…
Comment: DESeq2 output used for PCA plot on R studio by ATpoint ★ 4.0k
> Increase variability for mutants: use larger subtractive modifiers I was thinking the same as swbarnes. You're doing some data munging h…
Comment: minfi::read.metharray.exp by Basti ▴ 780
This is indeed correct now !
Comment: get BM error by Fara • 0
Thank you for the reply. The examples are these. ENSGACG00000014473 ENSGACG00000015168 ENSGACG00000007529
Comment: get BM error by Mike Smith ★ 6.5k
Can you provide an example of the Ensemble IDs you're trying to convert?
Votes
Comment: get BM error
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
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