Showing : covariates • reset
3
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19
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3.6k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma batch effect covariates contrast differential gene expression
7.1 years ago mheydarpour ▴ 10
5
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10
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2.0k
views
EdgeR full model vs. reduced model - p-value for covariate
EdgeR differential expression analysis covariates
updated 3.8 years ago by 50k • written 3.8 years ago by ▴ 60
5
votes
9
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1.7k
views
limma Multi-level Experiments correcting for continuous covariates
limma epic methylation limma design matrix covariates
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
5
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8
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8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 2 days ago by • 0 • written 7.7 years ago by ▴ 30
0
votes
4
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2.5k
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DESeq2: Outliers, covariates and number of replicates
deseq2 ruvseq cookscutoff covariates batch
7.4 years ago j.viana • 0
2
votes
4
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4.8k
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Age covariate continuous vs. categorical
deseq2 linear model covariates age design model
updated 6.3 years ago by 41k • written 6.3 years ago by • 0
1
vote
4
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20k
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Adjusting for covariates in paired sample design DESeq2
deseq2 deseq paired samples covariates multiple time points
6.6 years ago imb ▴ 10
3
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4
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953
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How to check whether experimental covariates are confounded with our group of interest?
covariates microarray
4.6 years ago english.server ▴ 20
3
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4
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1.2k
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Agilent Single-Channel Data: Questions about model statement and model building.
limma agilent microarray covariates
updated 6.0 years ago by 50k • written 6.0 years ago by ▴ 10
2
votes
3
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9.1k
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DESeq2 model with covariates
deseq2 covariates
updated 6.7 years ago by 41k • written 6.7 years ago by • 0
2
votes
3
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847
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Drug response pre- and post-treatment between timepoints across conditions
RNA-seq Paired design Timecourse Diagnosis Covariates
updated 4.1 years ago by ★ 3.9k • written 4.1 years ago by • 0
3
votes
3
replies
3.2k
views
Adjustment of covariates in 450k data using Limma
limma covariates 450k
8.1 years ago AST ▴ 60
2
votes
3
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1.4k
views
comBat/SVA with no "variable of interest" and two batches
combat sva covariates
updated 8.0 years ago by ▴ 420 • written 8.0 years ago by • 0
0
votes
3
replies
985
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
4
votes
3
replies
9.4k
views
How do I extract read counts from DESeq2
deseq2 counts covariates
updated 8.1 years ago by 41k • written 8.1 years ago by ▴ 10
0
votes
2
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1.6k
views
Removing batch effect from gene expression before Limma linear modelling
Limma differential gene expression batch effect correction covariates
updated 5.9 years ago by 50k • written 5.9 years ago by • 0
1
vote
2
replies
1.9k
views
RUVSEq and VSD integration
deseq2 ruvseq covariates continuous vsd
updated 8.1 years ago by 41k • written 8.1 years ago by ▴ 10
2
votes
2
replies
833
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2 vst covariates
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 20
0
votes
2
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3.1k
views
LIMMA Adjustment for Covariates
limma covariates
updated 8.3 years ago by ★ 28k • written 8.3 years ago by • 0
0
votes
1
reply
883
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2 rna-sequencing covariates glm
updated 4.4 years ago by 41k • written 4.4 years ago by ▴ 20
0
votes
1
reply
1.6k
views
DESeq2 biological replicates and RIN values
deseq2 differential gene expression covariates rnaseq
updated 6.6 years ago by 41k • written 6.6 years ago by • 0
0
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0
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488
views
Model matrix for a complex study design using aldex.glm module from ALDEx2 R package
ALDEx2 modelmatrix covariates
9 months ago amir • 0
0
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0
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1.8k
views
limma: blocking factors and factorial design
limma differential gene expression design and contrast matrix covariates
8.3 years ago jlerga • 0
0
votes
0
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935
views
How to specify covariates in maSigPro analysis (like limma)
masigpro covariates limma differential expression time-course
6.6 years ago veersingh.marwah • 0
24 results • Page 1 of 1
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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