Showing : DESE • reset
2
votes
2
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517
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Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
4 months ago BioinfGuru ▴ 70
0
votes
1
reply
365
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collapseReplicates dimension error
DESeq2 Dese
updated 9 months ago by 43k • written 9 months ago by • 0
0
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3
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524
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DESeq2 Results in Different Pvalue & Log2FC using the same code and data
DESeq2 dese
written 10 months ago by • 0
0
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2
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541
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Cross-species analysis using DESeq2 - size factor computation
dese DESeq2
11 months ago pl23 • 0
0
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2
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816
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Linear Model Fitting and Colinearity
dese DESeq2
12 months ago Hugo • 0
0
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5
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1.1k
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DESeq2 analysis
DESe DESeq2
17 months ago Adèle • 0
0
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2
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1.6k
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Handling NA's in Deseq2
Dese DESeq2
19 months ago Asger Mølgaard • 0
2
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17
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2.5k
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lfcshrink error DESeq2
DESeq2 lfcshrink DESe
updated 20 months ago by 43k • written 20 months ago by • 0
4
votes
5
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1.7k
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Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2 Dese DifferentialRegulation differe
updated 6 months ago by • 0 • written 21 months ago by ▴ 10
3
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3
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1.1k
views
Merging two plated in R
dese DESeq2
updated 2.6 years ago by 67k • written 2.6 years ago by ▴ 10
0
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5
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4.0k
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Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
DESE DESeq2
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by • 0
1
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3
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1.7k
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ERROR: unable to find an inherited method for function ‘dispersions<-’ for signature ‘"DESeqDataSet",
DESeq2 dese
2.9 years ago aedavids ▴ 20
0
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2
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1.0k
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DESeq2 ratio of ratios and p-value
DESeq2 dese
3.2 years ago wilfried.guiblet • 0
0
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2
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776
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where the gene is overexpressed and down regulated while doing DESeq2 analysis
DESe DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
2
votes
3
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1.2k
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Single sided P-value for DESeq2 Likelihood Ratio Test
DESeq2 DESe
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
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2
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1.0k
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Effect of within-group variation on gene expression analysis
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
16 results • Page 1 of 1
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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
It is not possible to use both. estimateGLMRobustDisp() estimates negative binomial dispersions for each gene, whereas glmQLFit() estimates…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0
Thank you. What is the difference between setting robust=TRUE in glmQLFit and estimateGLMRobustDisp? The paper i mentioned in the post used…
Comment: PCA of different bacterial species by Jeremy • 0
Your approach of using ~2500 single-copy orthologs and normalizing with VST or rlog for PCA is valid for exploring general clustering [pap…
Comment: RnBeads::combine() - error? by Urotree • 0
pheno <- rnb.set.arrays@pheno # Phenotypic data sites <- rnb.set.arrays@sites # CpG site definitions (data.frame) meth <- rnb.set…
Comment: RnBeads::combine() - error? by Urotree • 0
![enter image description here][1] [1]: /media/images/40d9778d-b044-4405-9b3d-2ba835f6 Hi, after I convert to RnBiseqSet, it shows "All…
Votes
C: How does edgeR cpm function calculate log(CPM) values?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
scater/scran with TPMs from Salmon - counts?
A: Full length single-cell RNA-seq - tximport output for downstream analysis
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