Showing : DEseq2 • reset
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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 18 months ago by ★ 5.0k • written 19 months ago by • 0
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3
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712
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
3
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1
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882
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 19 months ago by 43k • written 19 months ago by ▴ 10
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2
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987
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
19 months ago Aurora • 0
0
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1
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570
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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1
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458
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putting my own expression data in deseq2
DESeq2
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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3
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1.1k
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 19 months ago by ★ 5.0k • written 19 months ago by ▴ 10
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2
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735
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PCA plot suggestions
DESeq2 PCAtools
updated 19 months ago by 43k • written 19 months ago by • 0
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3
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1.1k
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 19 months ago by 43k • written 19 months ago by • 0
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9
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1.8k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 19 months ago by 68k • written 19 months ago by • 0
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848
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 19 months ago by 43k • written 19 months ago by • 0
1
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3
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756
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Different Shrunk Log2FC according with reference
DESeq2
updated 19 months ago by 43k • written 19 months ago by ▴ 20
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4
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1.1k
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
19 months ago winwater0928 • 0
3
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1
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870
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 19 months ago by 43k • written 19 months ago by ▴ 40
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7
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2.7k
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 19 months ago by ★ 1.4k • written 19 months ago by • 0
3
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3
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1.1k
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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1
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456
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rlog transformation
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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1
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1.3k
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 19 months ago by 43k • written 19 months ago by • 0
1
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2
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3.4k
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
19 months ago Patadù ▴ 20
0
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1
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431
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covariate with negative and positive values
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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1
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450
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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4
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953
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
19 months ago lonn • 0
0
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3
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750
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 19 months ago by 43k • written 19 months ago by ▴ 20
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2
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944
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How to retrieve detailed regression results from deseq2
DESeq2
19 months ago Weiqian ▴ 10
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4
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957
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DEG with low counts
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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1
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418
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Deseq2 Rlog transformation
DESeq2
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
1
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2
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793
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Design Matrix within group comparison more than two groups
DESeq2
19 months ago hemantcnaik • 0
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1
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623
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Bioinformatics student
Des DESeq2
updated 19 months ago by • 0 • written 19 months ago by • 0
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1
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754
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DESeq2 gives an error and R crashes
DESeq2
19 months ago Shefali • 0
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2
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821
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 19 months ago by 43k • written 19 months ago by ▴ 70
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1
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841
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 19 months ago by 43k • written 19 months ago by • 0
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2
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764
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Regressing out batch effects
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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2
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1.0k
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
1
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1
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835
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DESeq2 - Missing values in count matrix
DESeq2
updated 19 months ago by 68k • written 19 months ago by • 0
1
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6
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1.6k
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 20 months ago by 43k • written 20 months ago by • 0
1
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1
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507
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
20 months ago Layal • 0
0
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2
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732
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
20 months ago michelafrancesconi8 • 0
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4
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1.1k
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
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1
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441
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
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4
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1.4k
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PCA of different bacterial species
DESeq2
written 20 months ago by ▴ 10
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1
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600
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collapseReplicates dimension error
DESeq2 Dese
updated 20 months ago by 43k • written 20 months ago by • 0
3
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2
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771
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
20 months ago Anita ▴ 10
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879
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
20 months ago Chanderkant Chaudhary • 0
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2
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2.0k
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
20 months ago kcarey • 0
2
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3
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829
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 20 months ago by 43k • written 20 months ago by ▴ 20
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3
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937
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Help with Complex DESeq2 Design
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
1
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1
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703
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Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2 ctsGE
updated 20 months ago by 43k • written 20 months ago by • 0
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1
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444
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Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 20 months ago by 43k • written 20 months ago by • 0
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1
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1.5k
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
2
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2
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775
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With DESeq2 "Not full rank" Error with design
DESeq2 DEs
20 months ago feather-W • 0
4,839 results • Page 6 of 97
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Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Answer: p.adjust BH Question by Gordon Smyth 53k
Duplicate of https://support.bioconductor.org/p/41077/
Answer: Large logFC but somewhat high FDR by Gordon Smyth 53k
Glad you're getting good use out of the package. The results that you show seem pretty much as one would expect, with nothing surprising. …
Comment: After running samtools, the featureCounts command crashed. by MarcHintz99 • 0
Thanks for shairng https://subread.sourceforge.net/
Comment: Senior Teaching Fellow (MSc Computational Biomedicine) by eja.ger.m • 0
Opportunities like this remind me how digital learning is evolving, much like modern mobile games. With programmes becoming fully online an…
Votes
Comment: upstream git branches of bioc-release
A: p.adjust BH generates duplicate values
Answer: gene Set with high AUC score but no cells assigned to cell type
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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