Showing : DESEQ2 • reset
9
votes
9
replies
4.5k
views
Using Age or other numerical variable to model expression in deseq2
DESeq2
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
0
votes
4
replies
1.8k
views
I got error message about DESeqDataSetFromMatrix
DESeq2
updated 3.4 years ago by ★ 1.4k • written 3.4 years ago by • 0
2
votes
6
replies
2.0k
views
DESeq2: relevel() unsuccessfully setting control group
DESeq2
updated 3.4 years ago by • 0 • written 4.7 years ago by ▴ 30
1
vote
3
replies
3.0k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
2
votes
8
replies
2.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
3.4 years ago Kelen ▴ 10
4
votes
3
replies
3.3k
views
Large difference between lfcshrink and non-shrunk DESeq2 results
DESeq2
3.4 years ago Dave ▴ 10
0
votes
20
replies
3.4k
views
Different DESeq2 results (both FC and pvalue) by changing col/row orders in input
DESeq2
3.4 years ago Weisheng • 0
2
votes
4
replies
2.3k
views
deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
updated 8 months ago by 43k • written 3.4 years ago by ▴ 10
3
votes
3
replies
1.4k
views
Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
votes
1
reply
772
views
Interpretation of comparison results in nested designs
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 10
1
vote
3
replies
2.0k
views
Error in shrinkage for DESeq2
sva DESeq2
3.4 years ago Kent • 0
1
vote
3
replies
1.3k
views
Obtaining many more significant differentially expressed genes by subsetting than just using contrasts
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 10
0
votes
1
reply
712
views
Is my design bad for accounting for Batch Effect in DESEQ2?
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
vote
1
reply
822
views
roughDispEstimate and momentsDispEstimate
estimator roughmethodofmoments DESeq2 R Code
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
0
votes
5
replies
1.4k
views
problem withDESeq2
DESeq2
updated 3.4 years ago by ▴ 70 • written 3.4 years ago by • 0
1
vote
5
replies
1.8k
views
Error in DESeqDataSetFromMatrix
DESeq2
3.4 years ago fnu.chelsea • 0
0
votes
1
reply
971
views
lfc Shrinkage with multiple comparison groups
RNAseq lfcShrinkage DESeq2
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
0
votes
1
reply
758
views
Multifactor analysis
DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
vote
3
replies
872
views
DESeq2 changing Interaction term interpretation
DESeq2
written 3.4 years ago by • 0
0
votes
1
reply
774
views
Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
votes
2
replies
1.0k
views
Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
vote
1
reply
1.1k
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
vote
3
replies
1.1k
views
summary function when applying lfcThreshold gives a different result than when operating on the result of the same
DESeq2
updated 3.4 years ago by 43k • written 3.5 years ago by • 0
2
votes
5
replies
1.3k
views
DE genes with zero counts
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
votes
3
replies
1.4k
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
1
vote
6
replies
1.5k
views
DESeq2 counts error in as.data.frame
DESeq2
updated 3.4 years ago by ▴ 100 • written 3.5 years ago by • 0
2
votes
2
replies
3.4k
views
Create TPM gene tables/dataframe from ReCount3
recount3 TCGA GTEx DESeq2
3.5 years ago David ▴ 20
6
votes
7
replies
3.3k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
3.5 years ago • updated 3.4 years ago lmrogers34 ▴ 10
0
votes
3
replies
3.6k
views
ENSEMBL to gene symbol
biomaRt DESeq2
updated 3.5 years ago by ★ 4.1k • written 3.5 years ago by • 0
4
votes
3
replies
3.0k
views
Log2FoldChange and normalized count values are not consistent?
Normalization DESeq2
3.5 years ago Karla ▴ 10
1
vote
7
replies
2.5k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 3.4 years ago by 43k • written 3.5 years ago by ▴ 60
0
votes
1
reply
1.1k
views
Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
3
votes
4
replies
8.7k
views
Dispersion plot -Interpretation -DESeq2
DESeq2
3.5 years ago suhanya ▴ 20
0
votes
5
replies
3.6k
views
GO enrichment with non-model organism, supplying GO mappings
clusterProfiler goseq topGO DESeq2
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 30
5
votes
4
replies
2.6k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
updated 9 months ago by • 0 • written 3.5 years ago by ▴ 30
0
votes
2
replies
3.6k
views
Deseq2 Time series - 2 treatments 1 control 6 Time Points
timecourse DESeq2
updated 3.5 years ago by ▴ 100 • written 3.5 years ago by • 0
3
votes
8
replies
5.3k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.6 years ago by ▴ 10
1
vote
1
reply
1.1k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 20
0
votes
1
reply
897
views
Creating DESeq object and choosing a contrast
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
3
votes
3
replies
1.3k
views
Merging two plated in R
dese DESeq2
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 10
3
votes
9
replies
3.2k
views
Warnings when using "ashr" in lfcshrinkage for DESeq2
RNASeq DESeq2
updated 2.9 years ago by • 0 • written 3.5 years ago by ▴ 20
2
votes
4
replies
3.9k
views
ashr vs apeglm for interaction data
lfcShrink DESeq2
3.5 years ago Ali Barry ▴ 40
1
vote
4
replies
1.3k
views
different results in DESeq2 when comparing groups in two ways
DESeq2
3.5 years ago zohreh.fazelan • 0
2
votes
1
reply
2.3k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 3.5 years ago by ★ 1.4k • written 3.5 years ago by ▴ 10
1
vote
2
replies
1.1k
views
DESeq2 paired design: Differential list comparing fold changes
DESeq2
3.5 years ago • updated 3.4 years ago athira • 0
3
votes
4
replies
2.1k
views
DESeq2: Extracting Averaged Counts Information from dds and rld
DESeq2
3.5 years ago vanbelj ▴ 30
0
votes
6
replies
1.9k
views
DESeq2, Calculate the size factor by using median-of-ratio
median DESeq2
3.5 years ago KEREN • 0
0
votes
1
reply
3.3k
views
The results(dds) function in DESeq2 gives Na values for padj
DESeq2
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
0
votes
1
reply
979
views
miRNA analysis with DESeq2
mirna DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
votes
4
replies
1.2k
views
different sample size from each individual
DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
4,838 results • Page 21 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 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
United States, 1 minute ago
Canada, 11 minutes ago
United States, 22 minutes ago
WEHI, Melbourne, Australia, 27 minutes ago
United States, 35 minutes ago
Traffic: 593 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