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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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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884
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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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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
19 months ago Aurora • 0
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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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460
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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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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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PCA plot suggestions
DESeq2 PCAtools
updated 19 months ago by 43k • written 19 months ago by • 0
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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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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
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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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1.1k
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
19 months ago winwater0928 • 0
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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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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
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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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456
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rlog transformation
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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1.3k
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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
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
19 months ago Patadù ▴ 20
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433
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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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451
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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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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
19 months ago lonn • 0
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3
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752
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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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949
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How to retrieve detailed regression results from deseq2
DESeq2
19 months ago Weiqian ▴ 10
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959
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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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419
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Deseq2 Rlog transformation
DESeq2
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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794
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Design Matrix within group comparison more than two groups
DESeq2
19 months ago hemantcnaik • 0
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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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754
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DESeq2 gives an error and R crashes
DESeq2
19 months ago Shefali • 0
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 19 months ago by 43k • written 20 months ago by ▴ 70
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845
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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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764
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Regressing out batch effects
DESeq2
updated 19 months ago by 43k • written 20 months ago by • 0
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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 20 months ago by 68k • written 20 months ago by • 0
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837
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DESeq2 - Missing values in count matrix
DESeq2
updated 20 months ago by 68k • written 20 months ago by • 0
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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
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511
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
20 months ago Layal • 0
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2
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733
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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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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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442
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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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1.4k
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PCA of different bacterial species
DESeq2
written 20 months ago by ▴ 10
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603
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collapseReplicates dimension error
DESeq2 Dese
updated 20 months ago by 43k • written 20 months ago by • 0
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773
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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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883
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
20 months ago Chanderkant Chaudhary • 0
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2.0k
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
20 months ago kcarey • 0
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3
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831
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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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942
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Help with Complex DESeq2 Design
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
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706
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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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445
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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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1.5k
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
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2
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777
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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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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
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"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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