Showing : DESeq2 • reset
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 22 days ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 13 days ago by • 0 • written 16 months ago by ▴ 10
1
vote
2
replies
764
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
5 weeks ago • updated 26 days ago Patadù ▴ 10
0
votes
6
replies
594
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
6 days ago • updated 2 days ago Ken C • 0
0
votes
8
replies
554
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 8 days ago by ▴ 30 • written 9 days ago by • 0
1
vote
4
replies
537
views
DEseq2 coefficient
DESeq2 coefficient
12 weeks ago • updated 21 days ago JKim • 0
2
votes
7
replies
442
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
15 days ago • updated 12 days ago sajadahmad41454 • 0
2
votes
9
replies
441
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 27 days ago by 66k • written 28 days ago by • 0
0
votes
8
replies
407
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 28 days ago by ★ 1.4k • written 29 days ago by • 0
1
vote
4
replies
365
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
29 days ago • updated 27 days ago winwater0928 • 0
3
votes
1
reply
334
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 29 days ago by 42k • written 29 days ago by ▴ 40
1
vote
3
replies
319
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 15 days ago by ★ 4.2k • written 21 days ago by • 0
0
votes
6
replies
312
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 19 days ago by ★ 1.4k • written 20 days ago by ▴ 130
0
votes
3
replies
309
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 21 days ago by 42k • written 22 days ago by • 0
4
votes
9
replies
308
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 7 days ago by ★ 4.2k • written 8 days ago by • 0
3
votes
3
replies
278
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 24 days ago by ★ 4.2k • written 24 days ago by ▴ 10
1
vote
2
replies
269
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
9 days ago • updated 6 days ago BioinfGuru ▴ 30
2
votes
3
replies
267
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 18 days ago by ★ 4.2k • written 19 days ago by • 0
1
vote
3
replies
261
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 26 days ago by 42k • written 27 days ago by • 0
3
votes
3
replies
261
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by • 0
1
vote
3
replies
243
views
Different Shrunk Log2FC according with reference
DESeq2
updated 29 days ago by 42k • written 29 days ago by ▴ 20
0
votes
3
replies
236
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 21 days ago by ★ 4.2k • written 21 days ago by • 0
0
votes
2
replies
231
views
PCA plot suggestions
DESeq2 PCAtools
updated 26 days ago by 42k • written 28 days ago by • 0
0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
21 days ago • updated 20 days ago kcarey • 0
2
votes
4
replies
214
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 2 days ago by 42k • written 5 days ago by • 0
1
vote
1
reply
199
views
Handling multiple differential expression comparisons
DESeq2
updated 18 days ago by 42k • written 19 days ago by ▴ 10
0
votes
1
reply
192
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 13 days ago by ★ 4.2k • written 13 days ago by • 0
0
votes
2
replies
182
views
DESeq2 v1.35.0
DESeq2
updated 20 days ago by 42k • written 20 days ago by • 0
0
votes
2
replies
176
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
23 days ago • updated 20 days ago Aurora • 0
0
votes
1
reply
169
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 28 days ago by 42k • written 28 days ago by • 0
1
vote
1
reply
161
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 22 days ago by 42k • written 23 days ago by • 0
0
votes
3
replies
151
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 8 days ago by 42k • written 8 days ago by • 0
0
votes
1
reply
143
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 22 days ago by 42k • written 23 days ago by • 0
0
votes
1
reply
142
views
putting my own expression data in deseq2
DESeq2
updated 23 days ago by ★ 4.2k • written 23 days ago by • 0
1
vote
3
replies
135
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 2 days ago by 66k • written 3 days ago by ▴ 720
1
vote
8
replies
135
views
Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
23 hours ago • updated 15 hours ago boczniak767 ▴ 720
0
votes
1
reply
120
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 14 days ago by ★ 4.2k • written 14 days ago by • 0
0
votes
1
reply
117
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 8 days ago by 42k • written 9 days ago by • 0
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Comment: Get gene symbols for a set of hg19 coordinates by pcantalupo ▴ 10
Now why didn't I think of that? I had tunnel vision thinking I needed to use an annotation package. Thank you ATpoint!
Comment: Not able to install any Bioconductor 3.18 package [unable to access index] by Konstantin • 0
It works with "Germany (Gottingen)"! Thanks!
Comment: Not able to install any Bioconductor 3.18 package [unable to access index] by mgdrnl • 0
I solved the problem installing the latest R version (4.4.0)
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Comment: miRTarRnaseq library
Answer: Get gene symbols for a set of hg19 coordinates
Answer: Get gene symbols for a set of hg19 coordinates
Comment: recount3 problem downloading data from source sra
Not able to install any Bioconductor 3.18 package [unable to access index]
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