Showing : deseq2 • reset
0
votes
2
replies
143
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 7 hours ago by • 0 • written 1 day ago by • 0
0
votes
1
reply
53
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
19 hours ago • updated 18 hours ago shaunpeterson • 0
1
vote
2
replies
227
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
4 days ago • updated 1 day ago BioinfGuru ▴ 30
4
votes
9
replies
234
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 1 day ago by ★ 4.1k • written 3 days ago by • 0
0
votes
3
replies
104
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 3 days ago by 42k • written 3 days ago by • 0
0
votes
8
replies
488
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 3 days ago by ▴ 30 • written 4 days ago by • 0
0
votes
1
reply
84
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 3 days ago by 42k • written 4 days ago by • 0
2
votes
7
replies
370
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
10 days ago • updated 7 days ago sajadahmad41454 • 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 8 days ago by • 0 • written 16 months ago by ▴ 10
0
votes
1
reply
162
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 8 days ago by ★ 4.1k • written 8 days ago by • 0
0
votes
1
reply
100
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 9 days ago by ★ 4.1k • written 9 days ago by • 0
1
vote
3
replies
303
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 10 days ago by ★ 4.1k • written 16 days ago by • 0
1
vote
1
reply
185
views
Handling multiple differential expression comparisons
DESeq2
updated 13 days ago by 42k • written 14 days ago by ▴ 10
2
votes
3
replies
254
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 13 days ago by ★ 4.1k • written 14 days ago by • 0
0
votes
6
replies
291
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 14 days ago by ★ 1.4k • written 15 days ago by ▴ 130
0
votes
2
replies
167
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
18 days ago • updated 15 days ago Aurora • 0
0
votes
2
replies
209
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
16 days ago • updated 15 days ago kcarey • 0
0
votes
2
replies
161
views
DESeq2 v1.35.0
DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
0
votes
3
replies
221
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 16 days ago by ★ 4.1k • written 16 days ago by • 0
0
votes
3
replies
300
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 16 days ago by 42k • written 17 days ago by • 0
1
vote
4
replies
527
views
DEseq2 coefficient
DESeq2 coefficient
12 weeks ago • updated 16 days ago JKim • 0
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 17 days ago by • 0 • written 4.6 years ago by ▴ 10
1
vote
1
reply
155
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 17 days ago by 42k • written 17 days ago by • 0
0
votes
1
reply
138
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 17 days ago by 42k • written 18 days ago by • 0
0
votes
1
reply
135
views
putting my own expression data in deseq2
DESeq2
updated 18 days ago by ★ 4.1k • written 18 days ago by • 0
3
votes
3
replies
268
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 19 days ago by ★ 4.1k • written 19 days ago by ▴ 10
0
votes
2
replies
226
views
PCA plot suggestions
DESeq2 PCAtools
updated 21 days ago by 42k • written 23 days ago by • 0
1
vote
2
replies
740
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 21 days ago Patadù ▴ 10
1
vote
3
replies
253
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 21 days ago by 42k • written 22 days ago by • 0
1
vote
4
replies
356
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
24 days ago • updated 22 days ago winwater0928 • 0
2
votes
9
replies
426
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 22 days ago by 65k • written 22 days ago by • 0
0
votes
8
replies
383
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 23 days ago by ★ 1.4k • written 24 days ago by • 0
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 23 days ago by 42k • written 23 days ago by • 0
1
vote
3
replies
235
views
Different Shrunk Log2FC according with reference
DESeq2
updated 23 days ago by 42k • written 24 days ago by ▴ 20
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 24 days ago by 42k • written 24 days ago by ▴ 40
3
votes
3
replies
250
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 24 days ago by 42k • written 25 days ago by • 0
0
votes
4
replies
263
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
4 weeks ago • updated 28 days ago lonn • 0
1
vote
2
replies
262
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 28 days ago Weiqian ▴ 10
0
votes
7
replies
447
views
DESeq filtering specific to contrasts
DESeq2
updated 28 days ago by 42k • written 3 months ago by • 0
2
votes
5
replies
791
views
DESeq2 setting significant p-value
DESeq2
updated 28 days ago by 42k • written 5.0 years ago by ▴ 10
0
votes
4
replies
292
views
DEG with low counts
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by • 0
0
votes
1
reply
157
views
rlog transformation
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by • 0
0
votes
1
reply
125
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 29 days ago by 42k • written 4 weeks ago by • 0
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by • 0
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 29 days ago by • 0 • written 8.9 years ago by ▴ 30
0
votes
1
reply
166
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by • 0
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 4 weeks ago by • 0 • written 11 months ago by • 0
0
votes
4
replies
629
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 4 weeks ago by 42k • written 6 months ago by • 0
0
votes
3
replies
229
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by ▴ 20
0
votes
1
reply
145
views
Deseq2 Rlog transformation
DESeq2
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards • All
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Popular Question to Johannes Rainer ★ 2.0k
Locations • All
Poland, 10 minutes ago
Hong Kong, 11 minutes ago
Greece, 21 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
United States, 1 hour ago
Traffic: 425 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