Showing : DeSeq2 • reset
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
35 minutes ago Eric Katagirya • 0
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15
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
3 hours ago piemmea • 0
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1
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86
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
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1
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75
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 4 days ago by ★ 4.1k • written 4 days ago by • 0
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7
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296
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
5 days ago • updated 2 days ago sajadahmad41454 • 0
1
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1
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160
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Handling multiple differential expression comparisons
DESeq2
updated 8 days ago by 42k • written 10 days ago by ▴ 10
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6
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258
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 9 days ago by ★ 1.4k • written 10 days ago by ▴ 130
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3
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223
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 8 days ago by ★ 4.1k • written 10 days ago by • 0
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2
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141
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DESeq2 v1.35.0
DESeq2
updated 11 days ago by 42k • written 11 days ago by • 0
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2
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189
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Deseq2 and Normalization of RNA sequencing data
DESeq2
11 days ago • updated 10 days ago kcarey • 0
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3
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195
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
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3
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279
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 5 days ago by ★ 4.1k • written 11 days ago by • 0
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3
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284
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 11 days ago by 42k • written 12 days ago by • 0
1
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1
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142
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 13 days ago by 42k • written 13 days ago by • 0
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2
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152
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
13 days ago • updated 10 days ago Aurora • 0
0
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1
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128
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 13 days ago by 42k • written 13 days ago by • 0
0
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1
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127
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putting my own expression data in deseq2
DESeq2
updated 13 days ago by ★ 4.1k • written 13 days ago by • 0
3
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3
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256
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 14 days ago by ★ 4.1k • written 14 days ago by ▴ 10
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2
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221
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PCA plot suggestions
DESeq2 PCAtools
updated 17 days ago by 42k • written 18 days ago by • 0
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3
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241
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 17 days ago by 42k • written 17 days ago by • 0
2
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9
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410
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 17 days ago by 65k • written 18 days ago by • 0
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1
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163
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 18 days ago by 42k • written 19 days ago by • 0
1
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3
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227
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Different Shrunk Log2FC according with reference
DESeq2
updated 19 days ago by 42k • written 19 days ago by ▴ 20
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4
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348
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
19 days ago • updated 17 days ago winwater0928 • 0
3
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1
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320
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 19 days ago by 42k • written 20 days ago by ▴ 40
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8
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369
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 18 days ago by ★ 1.4k • written 20 days ago by • 0
3
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3
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236
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 20 days ago by 42k • written 21 days ago by • 0
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1
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147
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rlog transformation
DESeq2
updated 25 days ago by 42k • written 25 days ago by • 0
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1
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120
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 25 days ago by 42k • written 25 days ago by • 0
1
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2
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726
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
26 days ago • updated 17 days ago ussarizona ▴ 10
0
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1
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139
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covariate with negative and positive values
DESeq2
updated 25 days ago by 42k • written 26 days ago by • 0
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1
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158
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 25 days ago by ★ 4.1k • written 26 days ago by • 0
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4
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248
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
26 days ago • updated 23 days ago lonn • 0
0
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3
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214
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 27 days ago by 42k • written 28 days ago by ▴ 20
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2
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250
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How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 24 days ago Weiqian ▴ 10
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4
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281
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DEG with low counts
DESeq2
updated 24 days ago by 42k • written 29 days ago by • 0
0
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1
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138
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Deseq2 Rlog transformation
DESeq2
updated 28 days ago by ★ 4.1k • written 29 days ago by • 0
1
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4
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500
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DEseq2 coefficient
DESeq2 coefficient
11 weeks ago • updated 12 days ago JKim • 0
0
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7
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436
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DESeq filtering specific to contrasts
DESeq2
updated 24 days ago by 42k • written 12 weeks ago by • 0
0
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4
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615
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 27 days ago by 42k • written 6 months ago by • 0
2
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5
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1.2k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 26 days ago by • 0 • written 11 months ago by • 0
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2
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1.5k
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 3 days ago by • 0 • written 15 months ago by ▴ 10
6
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19
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2.5k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 13 days ago by • 0 • written 4.6 years ago by ▴ 10
2
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5
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776
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DESeq2 setting significant p-value
DESeq2
updated 24 days ago by 42k • written 5.0 years ago by ▴ 10
9
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12
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7.8k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 25 days ago by • 0 • written 8.8 years ago by ▴ 30
45 results • Page 1 of 1
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Comment: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by alex.pico ▴ 20
Hi Matthew. Happy to help. The error message you are getting is indeed not very helpful. It's just saying that the CyREST return obj "res" …
Comment: ChipQC 'names' attribute [9] must be the same length as the vector [2]' by bandconductor • 0
thanks! you have saved me so much time
Comment: Problem finding certain variables when importing a public database GSE73103 by Guido Hooiveld ★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
Votes
Answer: ChipQC 'names' attribute [9] must be the same length as the vector [2]'
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
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