Showing : rna • reset
2
votes
7
replies
311
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 17 months ago by 58k • written 17 months ago by • 0
3
votes
6
replies
1.1k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA rna-seq science bioinformatics
updated 4.5 years ago by 58k • written 4.5 years ago by ▴ 20
0
votes
6
replies
239
views
Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 19 months ago by 34k • written 19 months ago by • 0
5
votes
5
replies
488
views
Association analysis between gene expression and Phenotype
rna singlecell limma
updated 2.6 years ago by ★ 27k • written 2.6 years ago by ▴ 20
6
votes
5
replies
2.1k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 20
5
votes
4
replies
727
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 4.4 years ago by • 0 • written 4.4 years ago by ▴ 30
0
votes
4
replies
318
views
Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma edgeR rna
6 months ago Nirad • 0
0
votes
4
replies
3.8k
views
RNAseq Adjusting for Covariates?
RNA rnaseq Covariate adjustment deseq
updated 5.6 years ago by 34k • written 5.6 years ago by • 0
0
votes
3
replies
354
views
Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 11 months ago by 43k • written 11 months ago by • 0
4
votes
3
replies
411
views
How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation rna
updated 12 months ago by 58k • written 12 months ago by ▴ 20
2
votes
3
replies
415
views
Number and percent of mapped reads from RNA seq analysis.
rna-seq rna
updated 2.6 years ago by 13k • written 2.6 years ago by ▴ 20
0
votes
2
replies
689
views
Normalizzation indipentent data from RNAAeq experiment
rna normalization
7.0 years ago aristotele_m ▴ 30
0
votes
2
replies
377
views
DESeq and checkFullRank(modelMatrix)
RNA DESeq2
updated 2.5 years ago by 34k • written 2.5 years ago by ▴ 10
0
votes
1
reply
962
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 4.2 years ago by 34k • written 4.2 years ago by ▴ 20
1
vote
1
reply
655
views
Outliers - to remove or to not remove that is the question
outliers rna microarray
updated 4.4 years ago by ▴ 390 • written 4.4 years ago by ▴ 30
1
vote
1
reply
344
views
how to filter genes in significant module?
RNA WGCNA filter
2.3 years ago modarzi ▴ 10
3
votes
1
reply
929
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 5.1 years ago by ★ 27k • written 5.1 years ago by • 0
2
votes
1
reply
287
views
DESeq2 statistic and design
deseq2 RNA
updated 2.5 years ago by 34k • written 2.5 years ago by ▴ 10
0
votes
1
reply
536
views
Time series comparison with DESEQ2
RNA rnaseq deseq2
updated 4.2 years ago by 34k • written 4.2 years ago by ▴ 20
1
vote
1
reply
184
views
How to interpret coefficients of time course modeled data with DESeq2?
deseq2 RNA
updated 17 months ago by 34k • written 17 months ago by • 0
1
vote
0
replies
417
views
Job: 1 Computational Biologist and 1 Molecular Biologist
computational biology molecular biology RNA r-loop ncRNA Job
3.0 years ago l.brown ▴ 10
0
votes
0
replies
124
views
Cross-cultivar RNA-seq analysis
RNA Normalization
5 months ago nancy • 0
0
votes
0
replies
303
views
Job: Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell RNA Data analysis Bioinformatics Job
2.3 years ago jmaanaki • 0
0
votes
0
replies
795
views
Finding candidate binding sites for RNA binding proteins in R
R bioconductor RNA mRNA RNA binding proteins
4.6 years ago Walter F. Baumann ▴ 10
0
votes
0
replies
420
views
R code for finding wobble/redundant positions in an RNA string
r code rna wobble
3.7 years ago fawazfebin ▴ 30
25 results • Page 1 of 1
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Replies
Comment: DESeq2 version by adeler001 • 0
ok thank you for your response
Answer: DESeq2 version by Michael Love 34k
RStudio makes no difference, DESeq2 is based on R version. You can look up specific releases of Bioconductor by changing the URL: ht…
Comment: Contrast treated samples against both scramble and untreated controls by Michael Love 34k
Yes, for a typical `model.matrix` setup it should give `c(0,-.5,1)`
Comment: Contrast treated samples against both scramble and untreated controls by oliver.ziff • 0
Thank you @mikelove ! Yes, averaging the difference between Knockdown vs scramble and Knockdown vs untreated is a much better solution. S…
Comment: ggtree install by Brock • 0
For what it's worth, I didn't want to update my R version (4.0.5) so I downgraded rvcheck to v. 0.1.8 using: `devtools::install_version('r…
Votes
Comment: Model matrix not full rank, then
Testing three-way interactions in DESeq2
Answer: Contrast treated samples against both scramble and untreated controls
Comment: DESeq2 Normalization
A: standard error value (lfcSE) returned by DeSeq2
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