Showing : batch effects • reset
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full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 4.1 years ago by 66k • written 4.1 years ago by • 0
0
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3
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873
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Problem with including batch effects in linear model in LIMMA- samples are removed
limma batch effects linear model
updated 4.4 years ago by 66k • written 4.4 years ago by ▴ 20
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2.0k
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adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
4.5 years ago anne.bozack • 0
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910
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DEG among experimental and control group in MAST
MAST DEG batch effects
4.7 years ago chendianyu • 0
0
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0
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715
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adding batch effects as a covariate in additive model in edgeR
edger batch effects
updated 4.9 years ago by 66k • written 4.9 years ago by • 0
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8
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1.4k
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Code to address batch effect in total number of reads/ sample for DEG using Ballgown
differential expression analysis ballgown r batch effects total number of reads
updated 5.7 years ago by 66k • written 5.7 years ago by • 0
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1.3k
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Batch correction with uncertain biological variables
sva svaseq batch effect batch effects batch effect correction
6.8 years ago vedran.franke • 0
1
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1.9k
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Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 6.9 years ago by 66k • written 6.9 years ago by ▴ 10
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2
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1.3k
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Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
deseq2 random effects batch effects RNA-seq rna-seq
updated 6.9 years ago by 42k • written 6.9 years ago by • 0
9 results • Page 1 of 1
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Comment: Trouble reading samplesheet in with diffbind to create dba by Mallory • 0
Thank you for your reply! There mustve been something wierd going on with my peak formats as you pointed out. I recalled all the peaks and …
Answer: Trouble reading samplesheet in with diffbind to create dba by Anthony • 0
I was struggling with this today too. For me it happened because my peak files were not in the correct format. The "10 elements" refers to …
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Votes
Answer: How to do DESeq2 on Kallisto Data
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
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