Showing : DESEq2 • reset
2
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Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 2.5 years ago by ▴ 10
0
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9
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2.7k
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ranking the DeSeq2 results using t-values?
DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 10
0
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3
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1.4k
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DESeq2 with nbinomGLM issues
DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 20
0
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3
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2.2k
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DESeq2 package unrecognized after downloading latest version of R: keep getting erros
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
1
reply
846
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Design formula for genotype-specific condition effects using ~group in the design
RNASeqData DifferentialExpression DESeq2
updated 2.4 years ago by 43k • written 2.5 years ago by • 0
0
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5
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1.3k
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Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout DESeq2
written 2.5 years ago by • 0
0
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4
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1.5k
views
DESEq2 Error: rows did not converge
DESeq2
2.5 years ago • updated 2.4 years ago andrebolerbarros ▴ 20
0
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2
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1.1k
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Can DESeq2 handle low number of samples and replicates?
DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
2
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5
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2.3k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 19 months ago by • 0 • written 2.5 years ago by • 0
1
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4
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1.6k
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Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
written 2.6 years ago by • 0
1
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3
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1.2k
views
DESeq: relaxing gene filtering thresholds increases mean-Sd correlation, but recovers many important genes
metaanalysis meanSd genefilter DESeq2
2.5 years ago Ndimensional ▴ 20
2
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8
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2.0k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
2.5 years ago Ndimensional ▴ 20
0
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5
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1.4k
views
Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
votes
1
reply
519
views
Is there a way to solve "the model matrix is not full rank", when just one of my sample is showing batch effect?
DESeq2
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
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17
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4.9k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 2.5 years ago by • 0 • written 8.2 years ago by • 0
0
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1
reply
728
views
DESeq2 how to extract expression values corresponding to log2FoldChange
DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
votes
1
reply
810
views
Comparing DGE between datasets with uneven sample sizes using DESeq2
unevensamplesizes ComparingDGEresults DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
1
vote
1
reply
719
views
Deseq contrast question
RNASeqData DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 10
0
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4
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1.2k
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Using different filtering steps in different iterations of DEseq2
DESeq2
2.5 years ago marinaw ▴ 20
1
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2
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934
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Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
2.5 years ago jovel_juan ▴ 30
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2
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1.1k
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Can DESeq2 handle huge variations in sequencing depth among samples?
HugevariationsinsequencingDepth DESeq2
2.5 years ago Gopinath • 0
0
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4
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2.0k
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Discrepancy between DESeq2 files produced in Galaxy and R(RStudio)
DESeq2
updated 22 months ago by • 0 • written 2.5 years ago by • 0
0
votes
1
reply
615
views
Several questions about the workflow using DESeq2 to process RNA data
DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by ▴ 20
1
vote
3
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4.9k
views
DeSEQ 2 Error: some values in assay are negative
Countmatrix negativeassay DESeq2
2.5 years ago dania.khalid • 0
2
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2
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1.4k
views
DESeq2 on multilevel design variable
DESeq2
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by • 0
0
votes
1
reply
1.1k
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DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
0
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2
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2.3k
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Handling NA's in Deseq2
Dese DESeq2
2.5 years ago Asger Mølgaard • 0
0
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2
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1.3k
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Remove duplicate genera in DEseq output?
DESeq2
updated 2.5 years ago by ▴ 760 • written 2.5 years ago by • 0
0
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2
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1.5k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
2.5 years ago dwas • 0
3
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6
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1.6k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
1
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2
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1.0k
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Normalized counts from LRT or Wald test?
DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
2
votes
1
reply
886
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
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2
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1.3k
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DoparParam() execution fails when foreach() works
clustermq doparallel DESeq2
2.5 years ago boris • 0
0
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2
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1.8k
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Nanostring data differential expression analysis: limma or DESeq2?
DESeq2 NanoStringDiff limma
2.5 years ago pg45863 ▴ 10
0
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1
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1.0k
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how to solve this error
DESeq2 GEO miRNAData
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
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4
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1.4k
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
2.5 years ago sreeshmaraj72 • 0
0
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1
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975
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DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by • 0
2
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9
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7.0k
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how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 7.7 years ago by ▴ 10
3
votes
3
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1.9k
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by ▴ 20
1
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2
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1.8k
views
Batch effect between biological replicates
BatchEffect DESeq2
2.5 years ago gtechbio ▴ 10
1
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3
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1.1k
views
Find if one gene has a significantly different Log2FC than a different gene
DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
0
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3
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1.3k
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Dispersion outliers genes
Dispersion DESeq2
2.5 years ago raya.fai ▴ 60
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1
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1.2k
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Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
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2
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2.0k
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about baseMean in DEseq2
DESeq2
written 4.3 years ago by ▴ 670
3
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3
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1.4k
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Rlog performed on tpm or raw transcript abundances?
DESeq2 rlog
written 3.0 years ago by • 0
0
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2
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1.1k
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Accounting for technical replicates in DESeq2
DESeq2
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by • 0
3
votes
1
reply
1.0k
views
Applying DESeq2 to (suspected) Poisson distributed gene expression data (in the case of pseudoreplication)
DESeq2
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
2
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1
reply
1.5k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
2
votes
7
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3.0k
views
optimHess problem in apeglm/DESeq2
DESeq2 apeglm
updated 2.6 years ago by 43k • written 2.6 years ago by ★ 5.0k
1
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2
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1.1k
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
4,839 results • Page 12 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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