Showing : Covariates • reset
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Model matrix for a complex study design using aldex.glm module from ALDEx2 R package
ALDEx2 modelmatrix covariates
10 months ago amir • 0
5
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10
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2.1k
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EdgeR full model vs. reduced model - p-value for covariate
EdgeR differential expression analysis covariates
updated 3.9 years ago by 50k • written 3.9 years ago by ▴ 60
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3
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869
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Drug response pre- and post-treatment between timepoints across conditions
RNA-seq Paired design Timecourse Diagnosis Covariates
updated 4.2 years ago by ★ 3.9k • written 4.2 years ago by • 0
0
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1
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910
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Assessing the influence of covariates on RNA-seq in DESeq2
deseq2 rna-sequencing covariates glm
updated 4.4 years ago by 42k • written 4.4 years ago by ▴ 20
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3
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1.0k
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In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 4.6 years ago by 25k • written 4.6 years ago by • 0
3
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4
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989
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How to check whether experimental covariates are confounded with our group of interest?
covariates microarray
4.7 years ago english.server ▴ 20
2
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2
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848
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Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2 vst covariates
updated 5.0 years ago by 42k • written 5.0 years ago by ▴ 20
5
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9
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1.7k
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limma Multi-level Experiments correcting for continuous covariates
limma epic methylation limma design matrix covariates
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
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2
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1.6k
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Removing batch effect from gene expression before Limma linear modelling
Limma differential gene expression batch effect correction covariates
updated 6.0 years ago by 50k • written 6.0 years ago by • 0
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 6.1 years ago by 50k • written 6.1 years ago by ▴ 10
2
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4
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4.9k
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Age covariate continuous vs. categorical
deseq2 linear model covariates age design model
updated 6.3 years ago by 42k • written 6.3 years ago by • 0
0
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0
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952
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How to specify covariates in maSigPro analysis (like limma)
masigpro covariates limma differential expression time-course
6.7 years ago veersingh.marwah • 0
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4
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21k
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Adjusting for covariates in paired sample design DESeq2
deseq2 deseq paired samples covariates multiple time points
6.7 years ago imb ▴ 10
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1
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1.7k
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DESeq2 biological replicates and RIN values
deseq2 differential gene expression covariates rnaseq
updated 6.7 years ago by 42k • written 6.7 years ago by • 0
2
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3
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9.3k
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DESeq2 model with covariates
deseq2 covariates
updated 6.8 years ago by 42k • written 6.8 years ago by • 0
3
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19
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3.6k
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remove batch effect and adjusted model for 4 covariates in Limma
limma batch effect covariates contrast differential gene expression
7.2 years ago mheydarpour ▴ 10
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4
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2.6k
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DESeq2: Outliers, covariates and number of replicates
deseq2 ruvseq cookscutoff covariates batch
7.5 years ago j.viana • 0
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8
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8.9k
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Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 4 weeks ago by • 0 • written 7.8 years ago by ▴ 30
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3
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1.5k
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comBat/SVA with no "variable of interest" and two batches
combat sva covariates
updated 8.1 years ago by ▴ 420 • written 8.1 years ago by • 0
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3
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3.2k
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Adjustment of covariates in 450k data using Limma
limma covariates 450k
8.2 years ago AST ▴ 60
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2
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1.9k
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RUVSEq and VSD integration
deseq2 ruvseq covariates continuous vsd
updated 8.2 years ago by 42k • written 8.2 years ago by ▴ 10
4
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3
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9.5k
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How do I extract read counts from DESeq2
deseq2 counts covariates
updated 8.2 years ago by 42k • written 8.2 years ago by ▴ 10
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1.8k
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limma: blocking factors and factorial design
limma differential gene expression design and contrast matrix covariates
8.4 years ago jlerga • 0
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2
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3.1k
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LIMMA Adjustment for Covariates
limma covariates
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
24 results • Page 1 of 1
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Replies
Comment: Normalisation using clinical traits in RNA seq using DESeq2 by sukeshinik5 • 0
Thank you, so much for the response. When we estimate factors of unwanted variable, which is the better options for factorisation of the va…
Comment: ChAMP not available for bioconductor 3.19 by Macsue • 0
Warning message:package ChAMP is not available for Bioconductor version 3.19 A version of this package for your version of R might be avail…
Comment: ChAMP not available for bioconductor 3.19 by Macsue • 0
> if (!require("BiocManager", quietly = TRUE)) + install.packages("BiocManager") Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by BioinfGuru ▴ 30
I would use biomaRt. This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output…
Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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