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
9 months ago amir • 0
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10
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2.0k
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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
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3
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844
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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
0
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1
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878
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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 41k • written 4.4 years ago by ▴ 20
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3
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984
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In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
3
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4
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951
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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
2
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2
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828
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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
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 5.6 years ago by ★ 28k • written 5.6 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 5.9 years ago by 50k • written 5.9 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 6.0 years ago by 50k • written 6.0 years ago by ▴ 10
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4
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4.8k
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Age covariate continuous vs. categorical
deseq2 linear model covariates age design model
updated 6.2 years ago by 41k • written 6.2 years ago by • 0
0
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0
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932
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How to specify covariates in maSigPro analysis (like limma)
masigpro covariates limma differential expression time-course
6.6 years ago veersingh.marwah • 0
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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
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1
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1.6k
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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
2
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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
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
7.1 years ago mheydarpour ▴ 10
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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
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8
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8.7k
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Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 17 hours ago by • 0 • written 7.7 years ago by ▴ 30
2
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3
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1.4k
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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
3
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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
8.1 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 8.1 years ago by 41k • written 8.1 years ago by ▴ 10
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3
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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
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limma: blocking factors and factorial design
limma differential gene expression design and contrast matrix covariates
8.3 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 8.3 years ago by ★ 28k • written 8.3 years ago by • 0
24 results • Page 1 of 1
Recent ...
Replies
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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