Showing : DESeq2 • reset
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
2 hours ago • updated 14 minutes ago boczniak767 ▴ 720
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3
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121
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 1 day ago by 66k • written 2 days ago by ▴ 720
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4
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202
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 1 day ago by 42k • written 4 days ago by • 0
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6
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578
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
5 days ago • updated 1 day ago Ken C • 0
4
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9
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302
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 6 days ago by ★ 4.1k • written 7 days ago by • 0
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3
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146
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 7 days ago by 42k • written 7 days ago by • 0
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2
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265
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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
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8
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543
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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
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1
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113
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 7 days ago by 42k • written 8 days ago by • 0
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1
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189
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 12 days ago by ★ 4.1k • written 12 days ago by • 0
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1
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116
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 13 days ago by ★ 4.1k • written 13 days ago by • 0
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7
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
14 days ago • updated 11 days ago sajadahmad41454 • 0
2
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3
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265
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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
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1
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197
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Handling multiple differential expression comparisons
DESeq2
updated 17 days ago by 42k • written 18 days ago by ▴ 10
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6
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309
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 18 days ago by ★ 1.4k • written 19 days ago by ▴ 130
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2
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176
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DESeq2 v1.35.0
DESeq2
updated 19 days ago by 42k • written 19 days ago by • 0
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2
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219
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Deseq2 and Normalization of RNA sequencing data
DESeq2
20 days ago • updated 19 days ago kcarey • 0
0
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3
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233
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 20 days ago by ★ 4.1k • written 20 days ago by • 0
1
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3
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316
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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 14 days ago by ★ 4.1k • written 20 days ago by • 0
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3
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308
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 20 days ago by 42k • written 21 days ago by • 0
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1
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161
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 22 days ago by 42k • written 22 days ago by • 0
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1
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141
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putting my own expression data in deseq2
DESeq2
updated 22 days ago by ★ 4.1k • written 22 days ago by • 0
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2
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174
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
22 days ago • updated 19 days ago Aurora • 0
0
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1
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142
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 22 days ago by 42k • written 22 days ago by • 0
3
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3
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276
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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
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3
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259
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 26 days ago by 42k • written 26 days ago by • 0
2
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9
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433
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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 27 days ago by • 0
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2
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230
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PCA plot suggestions
DESeq2 PCAtools
updated 25 days ago by 42k • written 27 days ago by • 0
0
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1
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168
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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
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3
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242
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Different Shrunk Log2FC according with reference
DESeq2
updated 28 days ago by 42k • written 28 days ago by ▴ 20
1
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4
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364
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
28 days ago • updated 26 days ago winwater0928 • 0
3
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1
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331
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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
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8
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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
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3
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256
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 29 days ago by 42k • written 29 days ago by • 0
1
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2
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762
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
5 weeks ago • updated 26 days ago Patadù ▴ 10
1
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4
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535
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DEseq2 coefficient
DESeq2 coefficient
12 weeks ago • updated 20 days ago JKim • 0
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 12 days ago by • 0 • written 16 months ago by ▴ 10
6
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19
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2.6k
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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
38 results • Page 1 of 1
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Comment: Slightly different count plots from R and spreadsheet by boczniak767 ▴ 720
Thank you, but now I have six black and six red boxes (3 black, 3 red, 3 black, 3 red) whereas for each timepoint I have two experimental v…
Comment: Slightly different count plots from R and spreadsheet by Michael Love 42k
I added `col` so you can see the different groups. I just want you to be able to see the raw data so you can infer which plot is correct.
Comment: Slightly different count plots from R and spreadsheet by boczniak767 ▴ 720
Thank you, the code you provided gives boxplots for each data-point for pooled samples?
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman by xuz • 0
Could you try the following code and see whether you have any errors mf="MouseMethylation-12v1-0_A2.csv" manifest=readmanifest(mf) What …
Answer: Slightly different count plots from R and spreadsheet by Michael Love 42k
I'm gonna guess something went wrong in libreoffice. Try also ``` with(prb1, plot(timepoint, count, col=as.integer(ln))) ```
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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