Showing : DEseq2 • reset
3
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7
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3.6k
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Is it possible to convert "DESeq2's normalized counts" to "DEGs"?
DESeq2 raw
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by ▴ 10
0
votes
2
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1.4k
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Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
3.0 years ago Konstantinos • 0
0
votes
2
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809
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Setting up contrasts within a dataset within conditions (across different genotype) and across conditions (for the same genotype)
DESeq2
3.0 years ago nrama • 0
2
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3
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2.2k
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Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
3.0 years ago mohammedtoufiq91 ▴ 10
2
votes
1
reply
1.3k
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How to interpret DESeq2's padj after setting lfcThreshold and the log2FC is greater than lfcThreshold?
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
0
votes
2
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1.5k
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Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
0
votes
1
reply
743
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DESeq2, normalization for within-sample comparison, and 3'-end RNAseq data
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
4
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2
replies
2.2k
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DESeq2 false positive result?
DESeq2
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by ▴ 10
1
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2
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1.4k
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Changing the sample order in the PCA plot
DESeq2
3.0 years ago turtle888 • 0
0
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2
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1.5k
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Remove low-expressed genes in DESeq2?
DESeq2 lowcountgenes deseq2 independent
written 3.0 years ago by • 0
2
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4
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5.8k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
3.0 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
754
views
NA value in padj but only for certain contrasts
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
1
vote
12
replies
3.7k
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normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2 edgeR limma
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 670
0
votes
1
reply
746
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DESeq2 : Using contrast in results vs performing complete independent analysis
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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2
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1.4k
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Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2 adjp Volcano LRT
written 3.0 years ago by ▴ 10
0
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1
reply
1.2k
views
Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2 interaction coefficient LinearModel RNASeq
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
0
votes
1
reply
893
views
Design structure
DESeq2 des
updated 3.0 years ago by 43k • written 3.1 years ago by • 0
1
vote
2
replies
1.2k
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Question about contrasts in DESeq2
DESeq2
3.1 years ago • updated 3.0 years ago marinaw ▴ 20
0
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1
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1.1k
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Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 3.0 years ago by 43k • written 3.1 years ago by • 0
0
votes
1
reply
861
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Strange dispersion plot with high outliers
DESeq2
updated 3.0 years ago by 43k • written 3.1 years ago by • 0
0
votes
1
reply
969
views
How to extract DeSeq2 results for the different groups?
DESeq2
updated 3.0 years ago by 43k • written 3.1 years ago by • 0
0
votes
1
reply
844
views
DESeq2 paired multifactor test
DESeq2 StatisticalMethod
updated 3.0 years ago by 43k • written 3.1 years ago by ▴ 10
1
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3
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1.7k
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Problem with DESeq2
DESeq2 apple-m1
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
0
votes
4
replies
1.5k
views
Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
written 3.0 years ago by • 0
0
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1
reply
1.7k
views
DESeq2 design function and downstream analyses
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
2
replies
1.3k
views
Filtering normalised counts
DESeq2
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
votes
1
reply
530
views
DESeq2 effect of interaction when using a grouping variable
DESeq2
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
1
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4
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1.1k
views
DESeq2 says my sampleinfo has linear combination error but I don't see it...
DESeq2
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by • 0
1
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2
replies
1.4k
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How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
3.0 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.3k
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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2
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1.5k
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ChIP-Seq Analysis: Comparing Unannotated Peaks with DESeq2
DESeq2 MACS2
3.0 years ago vanbelj ▴ 30
0
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5
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4.8k
views
Error with DESeq2: DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: character
DESeq2
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
0
votes
1
reply
825
views
Failed Construction of DESEQDataSet Object: C.Elegans
Celegans DESeq2 dds Errorinseq_len(length(idx)-1)
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
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2
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1.4k
views
DESeq2 correction for biological replicate variance using design
DESeq2
3.0 years ago lukas.krauss • 0
5
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18
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9.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 23 months ago by • 0 • written 3.8 years ago by • 0
0
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1
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1.1k
views
Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 3.1 years ago by ▴ 10 • written 3.1 years ago by • 0
1
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3
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2.1k
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Interpretation of LRT results
DESeq2 LRT Heatmap
updated 2.2 years ago by 68k • written 3.1 years ago by ▴ 10
0
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2
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979
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Include multiple factors in the DESeq formula design or subset data to analyze
DESeq2 multiple
3.1 years ago Yijing • 0
0
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6
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2.5k
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How to extract all comparison in DESeq2 LRT test
DESeq2 Likelihood-ratiotest
3.1 years ago Yijing • 0
0
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13
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3.6k
views
DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 3.0 years ago by 43k • written 3.1 years ago by ▴ 10
0
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1
reply
856
views
TOMOseq analysis
DESeq2 tomoda
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
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2
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1.3k
views
RNA-Seq Reads Count
DESeq2 htseq DEGseq RNASeq read
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
1
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3
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4.4k
views
DESeq2/genefilter compatibility with R 4.2.2
DESeq2 genefilter
3.1 years ago Morgane ▴ 10
1
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4
replies
1.2k
views
Paired analysis model
DESeq2
3.1 years ago giulia.lopatriello • 0
1
vote
1
reply
1.3k
views
Limit the number of nodes in DESeq2
DESeq2 BiocParallel
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by ▴ 10
2
votes
1
reply
1.1k
views
Different sequencing depth between replicates and samples
DESeq2 edgeR DiffBind
updated 3.1 years ago by 53k • written 3.1 years ago by ▴ 10
0
votes
3
replies
2.5k
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2 Toil RSEM
3.1 years ago Niveditha ▴ 20
1
vote
4
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3.3k
views
plotCounts to visualize variations of a specific genes along conditions
DESeq2 plotCounts vst
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 10
3
votes
12
replies
3.5k
views
Replicates in DESeq2
DESeq2
updated 3.1 years ago by • 0 • written 4.3 years ago by ▴ 10
1
vote
2
replies
1.5k
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 3.1 years ago by ★ 1.4k • written 3.1 years ago by • 0
4,839 results • Page 17 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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