Showing : DESEQ2 • reset
2
votes
2
replies
1.3k
views
Gene abundance DESEq
DESeq2
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
1
vote
3
replies
1.9k
views
Clarification about DESeq2 counts() function when dealing with covariates
DESeq2
updated 3.2 years ago by ★ 1.4k • written 3.2 years ago by • 0
0
votes
5
replies
6.4k
views
DESeq2 is not available for R version 4.2.1
DESeq2
3.2 years ago annamariabugaj ▴ 10
1
vote
2
replies
5.3k
views
Getting the normalized counts after running DESeq()
DESeq2 Normalization
updated 3.2 years ago by ▴ 10 • written 3.2 years ago by • 0
1
vote
2
replies
1.2k
views
DESEQ2 Normalisation Factor
DESeq2
3.2 years ago MAHESH • 0
0
votes
1
reply
846
views
DESeq2 : LRT with factorial and continuous data
DESeq2 DifferentialExpression
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
1
vote
6
replies
5.9k
views
Weird looking volcano plot
DESeq2 volcano
updated 3.1 years ago by 43k • written 3.2 years ago by • 0
0
votes
1
reply
927
views
Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
votes
2
replies
717
views
DESeq2 with incorrect adjusted Pvalues
DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
votes
2
replies
1.1k
views
Overwhelmed by DESEq2 options and how to answer my questions.: Two conditions and Three families
DESeq2
3.2 years ago lgspeight • 0
1
vote
3
replies
1.6k
views
different stat and p values when filtering or not by lfc in DESeq2
DESeq2 wald stat
updated 3.2 years ago by ▴ 760 • written 3.2 years ago by • 0
0
votes
3
replies
1.1k
views
code syntax for DESeq2 to derive DEGs from a complicated contrast or interaction contrast?
DESeq2 Complicated.contrast DEGs
updated 3.2 years ago by 43k • written 3.2 years ago by • -60
1
vote
1
reply
1.2k
views
What is the effect of passage number in the differential gene expression when performing RNA sequencing analysis?
DESeq2 passagenumber
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
1
vote
1
reply
874
views
How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
0
votes
2
replies
2.2k
views
clarification of the way of converting standard error to confidence interval for logFC in DESeq2 result table
DESeq2 Confidence.Interval
3.2 years ago Mike • -60
0
votes
1
reply
682
views
ref treatment
DESeq2
updated 3.2 years ago by ★ 1.4k • written 3.2 years ago by • 0
2
votes
1
reply
985
views
Time-series analyses of a multifactor design with DESeq2
DESeq2 MultipleFactors TimeSeriesExperiment
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
votes
4
replies
2.4k
views
DESeq2 lfcThreshold - all my padj are equal to 1
DESeq2 lfcThreshold
3.2 years ago Abir.khazaal ▴ 10
3
votes
2
replies
5.4k
views
Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 3.2 years ago by ★ 1.4k • written 3.2 years ago by • 0
5
votes
6
replies
2.5k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
0
votes
2
replies
2.0k
views
output file conversion from FeatureCount to DESeq2 - no duplicate for samples
DESeq2 FeatureCount
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
2
votes
3
replies
2.3k
views
DESeq2 contrasts using all relevant samples vs all samples
DESeq2
3.2 years ago jeffrey.maurer • 0
0
votes
7
replies
2.7k
views
DESeq2 Error in checkContrast(contrast, resNames) : when using list()
DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
5
votes
1
reply
900
views
Log2FC values slightly higher in some genes after DESeq2 shrinkage
DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
1
vote
3
replies
1.8k
views
resultsNames(dds) not showing all contrasts
DESeq2 resultsNames lfcShrink
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
1
vote
5
replies
2.2k
views
DESeq2 - Replacing outliers with continuous variable in design
DESeq2
updated 3.2 years ago by 43k • written 3.3 years ago by • 0
0
votes
5
replies
2.4k
views
DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 5 months ago by 43k • written 3.2 years ago by • 0
0
votes
3
replies
1.4k
views
Time course RNA seq with DESeq2
DESeq2
updated 3.2 years ago by ▴ 10 • written 3.3 years ago by • 0
0
votes
1
reply
756
views
DESeq2 analysis with 3 factors
DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
2
votes
1
reply
1.1k
views
How to make the data compatible for DESeq2?
DESeq2 TPM rawcounts StringTie
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 200
0
votes
1
reply
913
views
DESeq2 Design Matrix
DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 20
0
votes
4
replies
1.2k
views
DESeq2 likehood ratio
DESeq2
updated 3.2 years ago by 43k • written 3.3 years ago by ▴ 10
0
votes
1
reply
690
views
DESeq2 likehood ratio
DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
0
votes
1
reply
1.8k
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 3.2 years ago by 43k • written 3.3 years ago by • 0
0
votes
3
replies
1.7k
views
DESEq2 rerun gives different results
DESeq2
3.2 years ago Mia • 0
4
votes
5
replies
4.1k
views
Importance of Order in Design Formula
deseq2
updated 3.2 years ago by • 0 • written 6.3 years ago by • 0
1
vote
2
replies
793
views
how to plot the union of the 100 most expressed genes
DESeq2 RNASEQ
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
0
votes
1
reply
598
views
DESeq2 comparison of different sample combinations
DESeq2
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by • 0
1
vote
1
reply
1.1k
views
DESeq 2 failes to load
Bioconductor DESeq2
3.3 years ago Ruggero ▴ 10
2
votes
2
replies
1.1k
views
data import error
DESeq2
3.3 years ago • updated 3.2 years ago sumitra • 0
0
votes
2
replies
1.7k
views
DESeq2 on normalized data
DESeq2
3.3 years ago • updated 3.2 years ago lizaaa • 0
0
votes
1
reply
795
views
Differentially expressed genes from Deseq2 have similar counts
DESeq2
updated 3.3 years ago by ▴ 780 • written 3.3 years ago by • 0
0
votes
1
reply
644
views
Batch correction in deseq2
DESeq2
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by ▴ 40
0
votes
1
reply
1.4k
views
Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System
RNASeq Correlation DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
1
vote
3
replies
1.9k
views
Strange Dispersion plot
DESeq2
3.3 years ago • updated 3.2 years ago Yiqi ▴ 10
0
votes
1
reply
1.0k
views
Correlation between CpG methylation and gene expression from DESeq2-> Normalization of counts using VST + fpkm/rpkm for optimal normalization?
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
1
vote
4
replies
9.4k
views
TPM normalization starting with read counts
edgeR DESeq2
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
0
votes
1
reply
901
views
DESeq errpr in normalizePath
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
votes
2
replies
929
views
Question regarding averaging DESeq2 results.
DESeq2
3.3 years ago e.v.egeland • 0
0
votes
2
replies
1.3k
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
3.3 years ago Marie • 0
4,838 results • Page 19 of 97
Recent ...
Replies
Answer: mzR-Rcpp compiler version issue by Laurent Gatto 1.6k
There are two issues here. First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different …
Comment: Identifying differentially expressed genes in individual samples from a large co by jamie.gearing ▴ 60
Great. Yes, something descriptive is probably good enough, even if the p-values themselves are not so rigorous. Thanks very much Gordon!
Comment: Co-occurrence Network Analysis between Algae and Bacteria by Stefano Mangiola ▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
Answer: DESeq2 design for haplotype MPRA by aimesd808 • 0
I appreciate you telling me about this. Now it's crystal plain to me. Publish this: https://support.bioconductor.org/p/9162649/
Answer: Extract snp information from genomic regions with biomaRt -> "oaries_snp" by Kevin Blighe ★ 4.0k
My sincere apologies that my colleagues had ignored your question. The error occurs because the "chromosomal_region" filter is not valid…
Votes
Answer: Identifying differentially expressed genes in individual samples from a large co
Answer: Identifying differentially expressed genes in individual samples from a large co
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Comment: Error installing Seqinfo
Awards • All
Popular Question to shepherl 4.2k
Popular Question to Gordon Smyth 53k
Supporter to fabio.marroni • 0
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to James W. MacDonald 68k
Locations • All
United States, 23 minutes ago
United States, 37 minutes ago
Finland, 37 minutes ago
United States, 42 minutes ago
Pittsburgh, United States, 52 minutes ago
Traffic: 792 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