Showing : DESEQ2 • reset
3
votes
7
replies
1.6k
views
The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2 deseq
7.3 years ago blastzone.heimerdinger ▴ 20
0
votes
4
replies
1.6k
views
how do compare with DESeq2
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
votes
8
replies
2.8k
views
DESeq2 Multi factor, multi time point comparison design formula
rna-seq deseq2 deseq R
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
votes
1
reply
784
views
Cultivar+Time+Treatment study in Deseq2
bioconductor deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
votes
8
replies
4.9k
views
DESeq2: handling NA values in colData
deseq2 coldata NA
updated 15 months ago by 43k • written 7.3 years ago by ▴ 170
3
votes
1
reply
1.2k
views
DESeq2: Handling batch effects with only one control replicate coming from another batch
deseq2 rna-seq
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
votes
1
reply
1.4k
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
7
votes
4
replies
1.9k
views
DESeq2 error: "vector: cannot make a vector of mode 'S4'"
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 20
1
vote
4
replies
2.2k
views
Log2 fold-change shrinkage fails with lfcShrink when using the 'apeglm' method
deseq2 apeglm lfcshrink
7.3 years ago coulsonr ▴ 20
2
votes
6
replies
1.3k
views
accounting for technical variation in DESEQ2
deseq2 normalization
updated 7.3 years ago by ★ 3.0k • written 7.3 years ago by ▴ 10
1
vote
10
replies
2.9k
views
Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
deseq2 sequencing ribosome profiling riboseq multiple factor design
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
1
vote
9
replies
2.0k
views
DESeq2 - v1.18 different p-values from v1.20 (Is it minmu?)
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 20
1
vote
5
replies
7.9k
views
DESEq2 - Change reference level change "Contrasts" results
deseq2
7.3 years ago andrebolerbarros ▴ 20
0
votes
3
replies
874
views
A few up-regulated genes using an extravagant number of reads - effect on DE analysis
rnaseq deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
1
vote
7
replies
2.6k
views
skewed differentially expressed gene results - DESeq2
deseq2 differential gene expression outliers
updated 7.3 years ago by ★ 7.9k • written 7.3 years ago by ▴ 20
5
votes
9
replies
2.7k
views
DESeq2 baseMean from DiffBind summarizedExperiment
deseq2 diffbind basemean summarizedexperiment
7.3 years ago rbronste ▴ 60
2
votes
4
replies
9.9k
views
Adding gene names (or symbols) in my DESeq result
rnaseq gene names deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
6
votes
4
replies
4.3k
views
[DESeq2] Extracting results based on set thresholds
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
0
votes
3
replies
2.1k
views
Dose-response study with DESeq2 and no dose replicates
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
votes
6
replies
1.0k
views
DESeq2 / How to visualize differences into control conditions
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
votes
1
reply
1.1k
views
DESeq2 intstallation error on fedora
deseq2 R fedora qiime
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
votes
3
replies
1.9k
views
RNA-seq data analysis with two species using DESeq2
DESeq2
updated 7.3 years ago by ★ 3.8k • written 7.3 years ago by ▴ 20
0
votes
3
replies
1.4k
views
time series RNA-seq allowing time offset between individuals
edgeR deseq2 rna-seq timecourse fittimeseries
updated 7.3 years ago by ★ 29k • written 7.3 years ago by • 0
0
votes
1
reply
2.0k
views
Deseq2 default Cooks distance threshold
Deseq2 outliers cookscutoff
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
5
votes
4
replies
2.7k
views
lfcShrink behavior with homogeneous expression dataset
deseq2 lfcshrink betaprior
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 110
0
votes
1
reply
1.6k
views
DESeq2/tximport 'duplicate rownames not allowed' error
tximport deseq2
7.3 years ago ctl • 0
14
votes
5
replies
25k
views
Dealing with genes that have Padj=NA
deseq2
updated 2.3 years ago by • 0 • written 9.9 years ago by ▴ 60
6
votes
4
replies
8.0k
views
DESeq2 with proteomics data
deseq2
updated 6 months ago by • 0 • written 7.3 years ago by ▴ 10
2
votes
5
replies
5.4k
views
Batch Effect Correction
batch effect removebatcheffect edgeR rld DEseq2
7.3 years ago Antonio Ahn ▴ 10
1
vote
3
replies
1.8k
views
Help interpreting DESeq2 method for gene-wide dispersion estimates
deseq2 negative binomial model glm
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
votes
1
reply
736
views
DESeq2 with too many rejections
deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 20
2
votes
4
replies
765
views
Extract x and y values from plotDispEsts
R deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
2
votes
1
reply
2.9k
views
Should I use alpine and can I convert the output back to counts?
alpine deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 20
0
votes
4
replies
2.5k
views
DESeq2 I installed from latest Bionconductor version is still old version
deseq2 R bioconductor
updated 7.3 years ago by ★ 1.1k • written 7.3 years ago by • 0
3
votes
9
replies
3.4k
views
DESeq2 Normalized Counts for Mfuzz
deseq2 rnaseq mfuzz
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 50
0
votes
2
replies
868
views
Times series - DE genes over the time of individual condition design matrix, LRT/Wald
deseq2
updated 7.3 years ago by 43k • written 7.4 years ago by ▴ 10
1
vote
2
replies
1.7k
views
DESeq2 package for R 3.3.3
deseq2 R 3.3.3
7.3 years ago valentina.losardo • 0
3
votes
9
replies
2.6k
views
deseq2 zeros in all treatments, fold change
deseq2
updated 7.3 years ago by 43k • written 7.4 years ago by ▴ 10
2
votes
2
replies
656
views
Assessing within-individual and between-individual variability
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
votes
3
replies
1.2k
views
DESeq2 use of LRT
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
3
votes
2
replies
1.2k
views
Comparisons of comparisons in DESeq2
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
1
vote
4
replies
1.4k
views
Multiple comparisons with DESeq2
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
0
votes
4
replies
908
views
Advice on DESeq2 design
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
votes
3
replies
1.5k
views
time-series, no replicates, no control groupe
deseq2 time-series without replicate
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
votes
1
reply
2.3k
views
DeSeq2 installation on ubuntu fails
deseq2 R ubuntu bioconductor rstudio
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
votes
1
reply
506
views
Help with design for 2 controls in infection time points with deseq2
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
3
votes
5
replies
1.1k
views
DESeq2: possible to compare read counts at single nucleotide level ?
deseq2 rnaseq
updated 7.4 years ago by 53k • written 7.4 years ago by • 0
1
vote
5
replies
2.2k
views
How do I stop DESeq2 from loading and additional errors related to the package.
r deseq2 error
updated 7.4 years ago by ★ 1.1k • written 7.4 years ago by • 0
0
votes
2
replies
3.3k
views
What are the different strategies to filter out low count genes?
rnaseq deseq2 differential gene expression
updated 7.4 years ago by ★ 13k • written 7.4 years ago by ▴ 80
0
votes
4
replies
3.4k
views
Design formula in DeSeq2 to control for a variable
deseq2
updated 4.9 years ago by 43k • written 7.4 years ago by • 0
4,839 results • Page 61 of 97
Recent ...
Replies
Comment: featureCounts -L: high unassigned:mapq fraction by insurancetaaddddaxrealty • 0
FeatureCounts can behave differently with ONT cDNA BAM files due to long read splice patterns, and many users compare settings or presets m…
Comment: A problem occurs when running the monocle2 by e.j.aaw.g.erm • 0
For gamers facing technical issues or errors in complex scripts, the Redz Hub script download provides a reliable tool to optimize performa…
Answer: How can I correctly use phyloseq with Docker? by Kevin Blighe ★ 4.0k
The Bioconductor version must be compatible with the R version. Bioconductor version 3.18 is compatible with R version 4.3. The Dockerfile …
Answer: Boolean Gate Combination for Any 2 Positive Events in flowWorkspace by Kevin Blighe ★ 4.0k
Your proposed code is correct and will achieve the desired outcome. The boolean filter expression `IFNg & TNFa | IFNg & IL2 | TNFa & IL2` i…
Answer: Guidance Requested on GCN Network Analysis and Module Enrichment in R by Kevin Blighe ★ 4.0k
The discrepancy between `final_exp1` and `final_exp2` could arise from several factors, despite matching dimensions. The `identical()` func…
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Supporter to fabio.marroni • 0
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to James W. MacDonald 68k
Locations • All
Pakistan, 21 minutes ago
Pakistan, 1 hour ago
WEHI, Melbourne, Australia, 3 hours ago
United States, 5 hours ago
United States, 6 hours ago
Traffic: 482 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