Showing : DEseq2 • reset
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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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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
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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
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3
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3.0k
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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 3.4 years ago by • 0
2
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8
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2.6k
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RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
3.4 years ago Kelen ▴ 10
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3
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3.3k
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Large difference between lfcshrink and non-shrunk DESeq2 results
DESeq2
3.4 years ago Dave ▴ 10
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20
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3.5k
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Different DESeq2 results (both FC and pvalue) by changing col/row orders in input
DESeq2
3.4 years ago Weisheng • 0
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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 3.4 years ago by ▴ 10
3
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3
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1.4k
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Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.4 years ago by 43k • written 3.5 years ago by • 0
0
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1
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777
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Interpretation of comparison results in nested designs
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 10
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3
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2.0k
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Error in shrinkage for DESeq2
sva DESeq2
3.5 years ago Kent • 0
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3
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1.3k
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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
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1
reply
717
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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
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1
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826
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roughDispEstimate and momentsDispEstimate
estimator roughmethodofmoments DESeq2 R Code
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by • 0
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5
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1.4k
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problem withDESeq2
DESeq2
updated 3.5 years ago by ▴ 90 • written 3.5 years ago by • 0
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5
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1.8k
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Error in DESeqDataSetFromMatrix
DESeq2
3.5 years ago fnu.chelsea • 0
0
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1
reply
975
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
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765
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Multifactor analysis
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
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3
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873
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DESeq2 changing Interaction term interpretation
DESeq2
written 3.5 years ago by • 0
0
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1
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777
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Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
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2
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1.0k
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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
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1
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1.1k
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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
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3
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1.1k
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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
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1.3k
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DE genes with zero counts
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
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3
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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
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6
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1.5k
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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
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3.4k
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Create TPM gene tables/dataframe from ReCount3
recount3 TCGA GTEx DESeq2
3.5 years ago David ▴ 20
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7
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3.3k
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Batch effect with one sample being in two batches
BatchEffect DESeq2
3.5 years ago • updated 3.4 years ago lmrogers34 ▴ 10
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3
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3.6k
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ENSEMBL to gene symbol
biomaRt DESeq2
updated 3.5 years ago by ★ 4.1k • written 3.5 years ago by • 0
4
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3
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3.1k
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Log2FoldChange and normalized count values are not consistent?
Normalization DESeq2
3.5 years ago Karla ▴ 10
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7
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2.5k
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RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 3.4 years ago by 43k • written 3.5 years ago by ▴ 60
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1.1k
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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
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4
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Dispersion plot -Interpretation -DESeq2
DESeq2
3.5 years ago suhanya ▴ 20
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5
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3.6k
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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
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4
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2.6k
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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
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2
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3.6k
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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
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DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.6 years ago by ▴ 10
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1.1k
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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
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902
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Creating DESeq object and choosing a contrast
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
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1.3k
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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
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Warnings when using "ashr" in lfcshrinkage for DESeq2
RNASeq DESeq2
updated 2.9 years ago by • 0 • written 3.5 years ago by ▴ 20
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4
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3.9k
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ashr vs apeglm for interaction data
lfcShrink DESeq2
3.5 years ago Ali Barry ▴ 40
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1.3k
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different results in DESeq2 when comparing groups in two ways
DESeq2
3.5 years ago zohreh.fazelan • 0
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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
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2
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DESeq2 paired design: Differential list comparing fold changes
DESeq2
3.5 years ago • updated 3.4 years ago athira • 0
3
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2.1k
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DESeq2: Extracting Averaged Counts Information from dds and rld
DESeq2
3.5 years ago vanbelj ▴ 30
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6
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1.9k
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DESeq2, Calculate the size factor by using median-of-ratio
median DESeq2
3.5 years ago KEREN • 0
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3.3k
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The results(dds) function in DESeq2 gives Na values for padj
DESeq2
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
0
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1
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982
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miRNA analysis with DESeq2
mirna DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
4,839 results • Page 21 of 97
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
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
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
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
Comment: upstream git branches of bioc-release
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