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Linear Models
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Data format after removing batch effects using linear model vs using comBat
microarray
SVA
ComBat
Linear models
Residuals
6.8 years ago
DataFanatic
▴ 10
0
votes
1
reply
989
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 4.4 years ago by
Kevin Blighe
★ 3.9k • written 4.5 years ago by
lucasmiranda42
• 0
0
votes
3
replies
904
views
DESeq2 accounting for two confounders with interaction in the design matrix
deseq2
design matrix
multi-confounders
linear models
rna-seq
updated 4.2 years ago by
Michael Love
42k • written 4.2 years ago by
mohamedrefaat.1.1992
• 0
0
votes
0
replies
841
views
Model problem using ballgown
ballgown
linear models
6.1 years ago
Yong Li
▴ 50
2
votes
1
reply
754
views
What is the "linear model" part used for in Limma?
Limma
R
Linear Models
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
christiangriffioen
• 0
5 results • Page
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Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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