Showing : DeSeq2 • reset
0
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3
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How can i fix this problem in R
S4Vectors DESeq2
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
0
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1
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1.8k
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Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
9
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9
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4.5k
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Using Age or other numerical variable to model expression in deseq2
DESeq2
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
0
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4
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1.8k
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I got error message about DESeqDataSetFromMatrix
DESeq2
updated 3.4 years ago by ★ 1.4k • written 3.4 years ago by • 0
2
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6
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2.1k
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DESeq2: relevel() unsuccessfully setting control group
DESeq2
updated 3.4 years ago by • 0 • written 4.7 years ago by ▴ 30
1
vote
3
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3.1k
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miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 3.4 years ago by 43k • written 3.5 years ago by • 0
2
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8
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2.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
3.4 years ago Kelen ▴ 10
4
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3
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3.3k
views
Large difference between lfcshrink and non-shrunk DESeq2 results
DESeq2
3.5 years ago • updated 3.4 years ago Dave ▴ 10
0
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20
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3.5k
views
Different DESeq2 results (both FC and pvalue) by changing col/row orders in input
DESeq2
3.5 years ago • updated 3.4 years ago Weisheng • 0
2
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4
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2.3k
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deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
updated 8 months ago by 43k • written 3.5 years ago by ▴ 10
3
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3
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1.4k
views
Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
votes
1
reply
778
views
Interpretation of comparison results in nested designs
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 10
1
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3
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2.0k
views
Error in shrinkage for DESeq2
sva DESeq2
3.5 years ago Kent • 0
1
vote
3
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1.3k
views
Obtaining many more significant differentially expressed genes by subsetting than just using contrasts
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 10
0
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1
reply
720
views
Is my design bad for accounting for Batch Effect in DESEQ2?
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
1
vote
1
reply
827
views
roughDispEstimate and momentsDispEstimate
estimator roughmethodofmoments DESeq2 R Code
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by • 0
0
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5
replies
1.4k
views
problem withDESeq2
DESeq2
updated 3.5 years ago by ▴ 90 • written 3.5 years ago by • 0
1
vote
5
replies
1.8k
views
Error in DESeqDataSetFromMatrix
DESeq2
3.5 years ago fnu.chelsea • 0
0
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1
reply
978
views
lfc Shrinkage with multiple comparison groups
RNAseq lfcShrinkage DESeq2
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
0
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1
reply
769
views
Multifactor analysis
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
1
vote
3
replies
875
views
DESeq2 changing Interaction term interpretation
DESeq2
written 3.5 years ago by • 0
0
votes
1
reply
780
views
Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
votes
2
replies
1.1k
views
Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
1
vote
1
reply
1.1k
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
1
vote
3
replies
1.1k
views
summary function when applying lfcThreshold gives a different result than when operating on the result of the same
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
2
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5
replies
1.3k
views
DE genes with zero counts
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
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3
replies
1.4k
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Controversial DESEQ2 results
phyloseq DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
1
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6
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1.5k
views
DESeq2 counts error in as.data.frame
DESeq2
updated 3.5 years ago by ▴ 100 • written 3.5 years ago by • 0
2
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2
replies
3.4k
views
Create TPM gene tables/dataframe from ReCount3
recount3 TCGA GTEx DESeq2
3.5 years ago David ▴ 20
6
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7
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3.3k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
3.5 years ago • updated 3.4 years ago lmrogers34 ▴ 10
0
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3
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3.6k
views
ENSEMBL to gene symbol
biomaRt DESeq2
updated 3.5 years ago by ★ 4.1k • written 3.5 years ago by • 0
4
votes
3
replies
3.1k
views
Log2FoldChange and normalized count values are not consistent?
Normalization DESeq2
3.5 years ago Karla ▴ 10
1
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7
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2.5k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 60
0
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1
reply
1.1k
views
Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
3
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4
replies
8.7k
views
Dispersion plot -Interpretation -DESeq2
DESeq2
3.5 years ago suhanya ▴ 20
0
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5
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3.6k
views
GO enrichment with non-model organism, supplying GO mappings
clusterProfiler goseq topGO DESeq2
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 30
5
votes
4
replies
2.6k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
updated 9 months ago by • 0 • written 3.5 years ago by ▴ 30
0
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2
replies
3.6k
views
Deseq2 Time series - 2 treatments 1 control 6 Time Points
timecourse DESeq2
updated 3.5 years ago by ▴ 100 • written 3.5 years ago by • 0
3
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8
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5.4k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.6 years ago by ▴ 10
1
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1
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1.1k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 20
0
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1
reply
904
views
Creating DESeq object and choosing a contrast
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
3
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3
replies
1.3k
views
Merging two plated in R
dese DESeq2
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 10
3
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9
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3.3k
views
Warnings when using "ashr" in lfcshrinkage for DESeq2
RNASeq DESeq2
updated 2.9 years ago by • 0 • written 3.5 years ago by ▴ 20
2
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4
replies
3.9k
views
ashr vs apeglm for interaction data
lfcShrink DESeq2
3.5 years ago Ali Barry ▴ 40
1
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4
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1.3k
views
different results in DESeq2 when comparing groups in two ways
DESeq2
3.5 years ago zohreh.fazelan • 0
2
votes
1
reply
2.3k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 3.5 years ago by ★ 1.4k • written 3.5 years ago by ▴ 10
1
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2
replies
1.1k
views
DESeq2 paired design: Differential list comparing fold changes
DESeq2
3.5 years ago • updated 3.4 years ago athira • 0
3
votes
4
replies
2.1k
views
DESeq2: Extracting Averaged Counts Information from dds and rld
DESeq2
3.6 years ago • updated 3.5 years ago vanbelj ▴ 30
0
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6
replies
1.9k
views
DESeq2, Calculate the size factor by using median-of-ratio
median DESeq2
3.6 years ago • updated 3.5 years ago KEREN • 0
0
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1
reply
3.3k
views
The results(dds) function in DESeq2 gives Na values for padj
DESeq2
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
4,840 results • Page 21 of 97
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Replies
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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