Showing : DESeq2 • reset
1
vote
1
reply
1.7k
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 14 months ago by 43k • written 14 months ago by • 0
0
votes
1
reply
392
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 14 months ago by ★ 1.4k • written 14 months ago by • 0
0
votes
1
reply
712
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
2
votes
1
reply
814
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 14 months ago by 43k • written 14 months ago by • 0
0
votes
2
replies
865
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
14 months ago Kucsera • 0
1
vote
1
reply
624
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
1
vote
9
replies
1.8k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 14 months ago by ▴ 40
4
votes
2
replies
1.5k
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 14 months ago by ★ 5.0k • written 14 months ago by ▴ 10
1
vote
5
replies
1.2k
views
Deseq2 Design
RNASeq DESeq2
updated 14 months ago by 68k • written 14 months ago by • 0
0
votes
5
replies
1.4k
views
p value is 0, padj is 0
DESeq2
14 months ago Wirayatida • 0
1
vote
2
replies
1.4k
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
14 months ago georgii.vdovin • 0
0
votes
7
replies
1.4k
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 14 months ago by • 0 • written 14 months ago by • 0
0
votes
1
reply
621
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 15 months ago by 43k • written 15 months ago by ▴ 20
0
votes
3
replies
920
views
DESeq2 - Comparing Comparisons
DESeq2
updated 14 months ago by 68k • written 15 months ago by • 0
0
votes
4
replies
1.1k
views
lfcShrink and alpha value
lfcShrink DESeq2
15 months ago anon • 0
2
votes
1
reply
993
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 15 months ago by 43k • written 15 months ago by • 0
0
votes
2
replies
558
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
0
votes
2
replies
587
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
15 months ago Anna • 0
1
vote
2
replies
885
views
Deseq2 res Function
DESeq2
updated 15 months ago by 68k • written 15 months ago by ▴ 10
0
votes
4
replies
844
views
Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
15 months ago NB • 0
0
votes
5
replies
899
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
0
votes
1
reply
647
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 15 months ago by 68k • written 15 months ago by • 0
1
vote
2
replies
568
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
15 months ago Denise • 0
0
votes
1
reply
490
views
eRNAs count
RNASeq DESeq2
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
0
votes
1
reply
705
views
DESeq2 rerun returns different results
DESeq2
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
0
votes
1
reply
598
views
Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 15 months ago by 43k • written 15 months ago by • 0
0
votes
1
reply
774
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
2
votes
2
replies
1.4k
views
Handling biological replicates in DESeq2
DESeq2
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
5
votes
3
replies
30k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 7.1 years ago by ▴ 30
1
vote
6
replies
1.8k
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 15 months ago by 43k • written 15 months ago by ▴ 10
0
votes
2
replies
632
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 16 months ago by • 0
4
votes
5
replies
1.7k
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
16 months ago LuciaNhu • 0
0
votes
1
reply
873
views
Average expression of genes across replicates
DESeq2
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
0
votes
0
replies
499
views
News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
16 months ago info ▴ 10
0
votes
11
replies
2.8k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 11 months ago by • 0 • written 16 months ago by • 0
0
votes
1
reply
604
views
Deseq to output continous sequencing data
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
1
vote
4
replies
1.6k
views
Adjusted p-values become NA when sub-setting samples
DESeq2
16 months ago txema.heredia • 0
3
votes
3
replies
1.8k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 16 months ago by • 0
0
votes
2
replies
1.2k
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 16 months ago by • 0
0
votes
1
reply
527
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
2
votes
3
replies
1.4k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
1
vote
4
replies
1.2k
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
16 months ago boczniak767 ▴ 740
0
votes
1
reply
422
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
16 months ago JY • 0
0
votes
1
reply
518
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
0
votes
2
replies
564
views
how to extract expression matrix post deseq2
DESeq2
written 16 months ago by • 0
0
votes
2
replies
580
views
Using Normalized Counts in DESeq2
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
3
votes
2
replies
749
views
When running contrasts, does it use normalized read counts?
DESeq2
16 months ago Katherine ▴ 20
0
votes
1
reply
465
views
How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
7
votes
4
replies
1.8k
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
16 months ago Eva ▴ 30
1
vote
4
replies
1.6k
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 16 months ago by ★ 5.0k • written 17 months ago by • 0
4,851 results • Page 3 of 98
Recent ...
Replies
Answer: GSEA error by James W. MacDonald 68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Answer: Unable to find ENTREZ IDs by James W. MacDonald 68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
Answer: Inconsistencies between accessor functions for TxDb databases with selected seql by a2a2hd42aa • 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
Votes
Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Awards • All
Popular Question to boczniak767 ▴ 740
Popular Question to shepherl 4.3k
Popular Question to Gordon Smyth 53k
Popular Question to Matan G. ▴ 60
Popular Question to Jaqueline • 0
Locations • All
Pakistan, just now
Canada, 51 minutes ago
United States, 2 hours ago
Chile, 2 hours ago
Barcelona, Spain, 4 hours ago
Traffic: 1256 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