Showing : DEseq2 • reset
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DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
3.3 years ago Marie • 0
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5
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3.5k
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Issues installing DESeq2 package with R version 4.2.1
DESeq2
3.3 years ago lucabartolinimd • 0
2
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2
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2.3k
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How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
4
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5
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3.5k
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Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
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1
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830
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Handling heterogeneous data in DESeq2: multiple covariates to control against
RNASeq DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
2
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5
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1.6k
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Detection of reference genes by Deseq2
lessAbs reference_genes DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
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5
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3.2k
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DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
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3
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1.6k
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Swish: contrasts and interactions
fishpond DESeq2
updated 2.6 years ago by 43k • written 3.3 years ago by • 0
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2
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1.1k
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Contradictory results in smallRNA differential expression analysis using DESeq2
SmallRNA DESeq2
3.3 years ago jucosie • 0
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1
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1.4k
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Dispersion estimates with DESeq2
dispersionestimates dispersion DESeq2 estimates deseq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
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6
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2.3k
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Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
3.3 years ago Weiqian ▴ 10
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1
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1.1k
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DESeq2 - Batch effect correction in 2 conditions + 2 genotypes + interaction term design
DESeq2
updated 3.3 years ago by 43k • written 3.4 years ago by • 0
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1
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1.3k
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CQN to DESeq2
cqn DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
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5
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1.5k
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what should be our references when 2 samples which I compare are treated and there is not any control?
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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1
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1.1k
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I have a query regarding differential gene expression using limma-voom.
RNASeqData DESeq2
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
2
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1
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1.1k
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Subsetting a DESeq object - gene-wise dispersions
DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by ▴ 20
0
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1
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997
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DESeq2 Interaction Term Error Occurred
interaction DESeq2
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by • 0
2
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7
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25k
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Install DESeq2
DESeq2
3.3 years ago Chris ▴ 20
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3
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1.8k
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DESeq2 - transcript length correction necessary when quantifying reads from ends of transcripts?
Transcriptomics DESeq2
3.3 years ago marius.wenzel • 0
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2
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2.2k
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DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
3.3 years ago fluentin44 • 0
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1
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1.3k
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Help with featureCounts
DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
3
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2
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1.4k
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
3.3 years ago manwar • 0
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8
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4.5k
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DESeq2 different log2FC and p-value filtering parameters results comparison
log2 DESeq2
3.4 years ago • updated 3.3 years ago User000 • 0
2
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4
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2.1k
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pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 3.3 years ago by 53k • written 3.4 years ago by ▴ 10
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5
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1.4k
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DeSeq2 Matched Analysis
RNASeq DESeq2
3.4 years ago • updated 3.3 years ago Andrea • 0
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2
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2.8k
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[DESeq2] setting LFC threshold
DESeq2
3.4 years ago Shail • 0
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1
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1.9k
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lfcShrink types for Volcano plots
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
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4
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1.5k
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Can I use limma::avereps to remove dupicated genes before conduct DEG based on RSEM Expected_count data?
limma RNASeq Expected_count DESeq2
3.4 years ago Yang Shi ▴ 10
0
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1
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800
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DESeq2: correct way to extract comparison of comparisons
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
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1
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597
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DESeq2 for CaptureSeq
CaptureSeq DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
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2.0k
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Iterating over a column within colData@listData
DESeq2 iterating SummarizedExperiment
3.4 years ago BioInfoBeginnerrr • 0
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3
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1.6k
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LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
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7
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2.9k
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DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
0
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9
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2.7k
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Questions about the false positives indicated by DESeq2 and QQ plot
pre-filterin DESeq2
updated 2.1 years ago by ▴ 10 • written 3.4 years ago by ▴ 10
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3
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2.7k
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ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest
DESeq2
updated 12 months ago by 43k • written 3.4 years ago by • 0
0
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1
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894
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DESeq2 LRT not returning genes
LRT linearmodels DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 30
1
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2
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3.0k
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DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink DESeq2 RNASeq lfcthreshold
3.4 years ago ClaudiaE • 0
1
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12
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4.5k
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How to use "p-value" instead of "p-adj value" in DESeq2
DESeq2
updated 2.1 years ago by ★ 1.5k • written 3.4 years ago by • 0
1
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1
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662
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Error message : DESeq2
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
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935
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result does not change after relevel
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
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14
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6.2k
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GenomeInfoDbData had non-zero exit status
DESeq2 RStudio GenomeInfoDbData hadnon-zeroexitstatus
updated 3.2 years ago by • 0 • written 3.4 years ago by • 0
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2
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920
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DESeq2 question
DESeq2
3.4 years ago Yu • 0
0
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4
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1.5k
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Multi-factorial Time-based design in DEseq2: defining full and reduced model
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
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1
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801
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how do singleton samples contribute to dispersion estimate in DESeq2?
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 10
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4
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7.2k
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Error message: Could not find function "DESeqDataSetFromMatrix"
DESeq2
3.4 years ago Md. Faridul • 0
0
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1
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797
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Error
DESeq2
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
2
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8
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5.0k
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How to get DESeq2 results for a list of genes
DESeq2
3.4 years ago Lucía ▴ 30
1
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1
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1.3k
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setting sizeFactors from scran :: caculateSumFactors.
scran DESeq2
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
0
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4
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1.9k
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Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
3.4 years ago uhlkatie • 0
0
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3
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2.3k
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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
4,839 results • Page 20 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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