Showing : singlecellexperiment • reset
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 3 months ago by 65k • written 3 months ago by • 0
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6
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546
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
3 months ago Dario Strbenac ★ 1.5k
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150
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rpk per cell saved in SCE object.
SingleCellExperiment
3 months ago JalapenoCornbread • 0
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925
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Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
4 months ago elgomez • 0
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3
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Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
updated 4 months ago by • 0 • written 4 months ago by • 0
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 6 months ago by • 0
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5
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836
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 0
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885
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
10 months ago Matvii Mykhailichenko • 0
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2
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
10 months ago Lluís Revilla Sancho ▴ 730
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3
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
12 months ago • updated 11 months ago mollyab12 • 0
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Combining and using 10x Genomics output in SingleCellExperiment Objects
SingleCellExperiment
written 5.0 years ago by ▴ 350
11 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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