Showing : deseq2 • reset
1
vote
3
replies
119
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 1 day ago by 66k • written 2 days ago by ▴ 720
2
votes
4
replies
199
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 1 day ago by 42k • written 4 days ago by • 0
0
votes
6
replies
572
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
5 days ago • updated 1 day ago Ken C • 0
4
votes
9
replies
301
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 5 days ago by ★ 4.1k • written 7 days ago by • 0
0
votes
3
replies
145
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 6 days ago by 42k • written 7 days ago by • 0
1
vote
2
replies
265
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
8 days ago • updated 5 days ago BioinfGuru ▴ 30
0
votes
8
replies
541
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 7 days ago by ▴ 30 • written 8 days ago by • 0
0
votes
1
reply
111
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 7 days ago by 42k • written 8 days ago by • 0
0
votes
1
reply
189
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 12 days ago by ★ 4.1k • written 12 days ago by • 0
0
votes
1
reply
116
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 13 days ago by ★ 4.1k • written 13 days ago by • 0
2
votes
7
replies
435
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
14 days ago • updated 10 days ago sajadahmad41454 • 0
2
votes
3
replies
265
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 17 days ago by ★ 4.1k • written 18 days ago by • 0
1
vote
1
reply
197
views
Handling multiple differential expression comparisons
DESeq2
updated 16 days ago by 42k • written 18 days ago by ▴ 10
0
votes
6
replies
309
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 18 days ago by ★ 1.4k • written 19 days ago by ▴ 130
0
votes
2
replies
176
views
DESeq2 v1.35.0
DESeq2
updated 19 days ago by 42k • written 19 days ago by • 0
0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
20 days ago • updated 19 days ago kcarey • 0
0
votes
3
replies
231
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 days ago by ★ 4.1k • written 20 days ago by • 0
1
vote
3
replies
313
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 14 days ago by ★ 4.1k • written 20 days ago by • 0
0
votes
3
replies
308
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 20 days ago by 42k • written 21 days ago by • 0
1
vote
1
reply
161
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
0
votes
1
reply
141
views
putting my own expression data in deseq2
DESeq2
updated 21 days ago by ★ 4.1k • written 22 days ago by • 0
0
votes
2
replies
174
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
22 days ago • updated 19 days ago Aurora • 0
0
votes
1
reply
142
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 21 days ago by 42k • written 22 days ago by • 0
3
votes
3
replies
276
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 23 days ago by ★ 4.1k • written 23 days ago by ▴ 10
1
vote
3
replies
259
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 25 days ago by 42k • written 26 days ago by • 0
2
votes
9
replies
432
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 26 days ago by 66k • written 26 days ago by • 0
0
votes
2
replies
230
views
PCA plot suggestions
DESeq2 PCAtools
updated 25 days ago by 42k • written 27 days ago by • 0
0
votes
1
reply
168
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 27 days ago by 42k • written 27 days ago by • 0
1
vote
3
replies
242
views
Different Shrunk Log2FC according with reference
DESeq2
updated 27 days ago by 42k • written 28 days ago by ▴ 20
1
vote
4
replies
363
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
28 days ago • updated 26 days ago winwater0928 • 0
3
votes
1
reply
330
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 28 days ago by 42k • written 28 days ago by ▴ 40
0
votes
8
replies
404
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 27 days ago by ★ 1.4k • written 28 days ago by • 0
3
votes
3
replies
256
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 28 days ago by 42k • written 29 days ago by • 0
1
vote
2
replies
762
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 25 days ago Patadù ▴ 10
1
vote
4
replies
534
views
DEseq2 coefficient
DESeq2 coefficient
12 weeks ago • updated 20 days ago JKim • 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 11 days ago by • 0 • written 16 months ago by ▴ 10
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 21 days ago by • 0 • written 4.6 years ago by ▴ 10
37 results • Page 1 of 1
Recent ...
Replies
Comment: recount3 problem downloading data from source sra by PABLO ANTONIO • 0
Hello Leonardo, Thanks for commenting on possible solutions. I noticed comparing your session info that I was using the previous version o…
Comment: seqlevelsStyle() not working by websterdelacruz2087055 • 0
Specify the new URL new_url <- "https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz" Use the new URL to download th…
Comment: SGSeq: moving toward diffex from SGSeq analysis by Sara • 0
Yes, thank you. I have another error now, may you please guide me. here is the code that I used till using vep: ```r # bam_path <- "~/pat…
Comment: slingshot: error with plot3d.SlingshotDataSet by Happiness • 0
Hi please i am encountering similar issue how did you fix it. Here is the code: ## Run Slingshot p3.neuron.sds <- slingshot(Embeddings(…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by mohammedtoufiq91 ▴ 10
https://support.bioconductor.org/u/5106/ thank you very much.
Votes
Answer: recount3 problem downloading data from source sra
Answer: recount3 problem downloading data from source sra
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
Awards • All
Scholar to Mike Smith ★ 6.5k
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to bas_work ▴ 30
Popular Question to landenshanie ▴ 40
Locations • All
Japan, 4 minutes ago
Germany, 6 minutes ago
Greece, 6 minutes ago
Egypt, 8 minutes ago
Belgium, 18 minutes ago
Traffic: 749 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