Showing : DESEq2 • reset
3
votes
7
replies
3.6k
views
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
replies
1.4k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
3.0 years ago Konstantinos • 0
0
votes
2
replies
809
views
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
votes
3
replies
2.2k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
3.0 years ago mohammedtoufiq91 ▴ 10
2
votes
1
reply
1.3k
views
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
replies
1.5k
views
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
744
views
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
votes
2
replies
2.2k
views
DESeq2 false positive result?
DESeq2
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by ▴ 10
1
vote
2
replies
1.4k
views
Changing the sample order in the PCA plot
DESeq2
3.0 years ago turtle888 • 0
0
votes
2
replies
1.5k
views
Remove low-expressed genes in DESeq2?
DESeq2 lowcountgenes deseq2 independent
written 3.0 years ago by • 0
2
votes
4
replies
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
756
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
views
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
views
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
votes
2
replies
1.4k
views
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
votes
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 3.1 years ago by ▴ 10
0
votes
1
reply
894
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
views
Question about contrasts in DESeq2
DESeq2
3.1 years ago • updated 3.0 years ago marinaw ▴ 20
0
votes
1
reply
1.1k
views
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
862
views
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
vote
3
replies
1.7k
views
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
votes
1
reply
1.8k
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
vote
4
replies
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
vote
2
replies
1.4k
views
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
votes
2
replies
1.5k
views
ChIP-Seq Analysis: Comparing Unannotated Peaks with DESeq2
DESeq2 MACS2
3.0 years ago vanbelj ▴ 30
0
votes
5
replies
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
votes
2
replies
1.4k
views
DESeq2 correction for biological replicate variance using design
DESeq2
3.1 years ago lukas.krauss • 0
5
votes
18
replies
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
votes
1
reply
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
vote
3
replies
2.1k
views
Interpretation of LRT results
DESeq2 LRT Heatmap
updated 2.2 years ago by 68k • written 3.1 years ago by ▴ 10
0
votes
2
replies
982
views
Include multiple factors in the DESeq formula design or subset data to analyze
DESeq2 multiple
3.1 years ago Yijing • 0
0
votes
6
replies
2.5k
views
How to extract all comparison in DESeq2 LRT test
DESeq2 Likelihood-ratiotest
3.1 years ago Yijing • 0
0
votes
13
replies
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
votes
1
reply
856
views
TOMOseq analysis
DESeq2 tomoda
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
votes
2
replies
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
vote
3
replies
4.4k
views
DESeq2/genefilter compatibility with R 4.2.2
DESeq2 genefilter
3.1 years ago Morgane ▴ 10
1
vote
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
replies
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
Recent ...
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
Awards • All
Popular Question to efoss ▴ 10
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Popular Question to story.benjamin ▴ 20
Locations • All
United States, 33 minutes ago
United States, 35 minutes ago
United States, 42 minutes ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 934 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6