Showing : DeSeq2 • reset
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
1
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3
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3.3k
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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 19 months ago by ★ 5.0k • written 19 months ago by • 0
0
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3
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718
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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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887
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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990
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
19 months ago Aurora • 0
0
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1
reply
574
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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
0
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1
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463
views
putting my own expression data in deseq2
DESeq2
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
3
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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
0
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2
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744
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PCA plot suggestions
DESeq2 PCAtools
updated 19 months ago by 43k • written 19 months ago by • 0
1
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3
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1.1k
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 19 months ago by 43k • written 19 months ago by • 0
2
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9
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1.8k
views
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
0
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1
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852
views
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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761
views
Different Shrunk Log2FC according with reference
DESeq2
updated 19 months ago by 43k • written 19 months ago by ▴ 20
1
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4
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1.1k
views
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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879
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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
views
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
replies
1.1k
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
0
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1
reply
457
views
rlog transformation
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
0
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1
reply
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
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
19 months ago Patadù ▴ 20
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1
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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
0
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1
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453
views
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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960
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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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757
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 19 months ago by 43k • written 19 months ago by ▴ 20
1
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2
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951
views
How to retrieve detailed regression results from deseq2
DESeq2
20 months ago • updated 19 months ago Weiqian ▴ 10
0
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4
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962
views
DEG with low counts
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
0
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1
reply
422
views
Deseq2 Rlog transformation
DESeq2
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
1
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2
replies
798
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Design Matrix within group comparison more than two groups
DESeq2
19 months ago hemantcnaik • 0
0
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1
reply
626
views
Bioinformatics student
Des DESeq2
updated 19 months ago by • 0 • written 19 months ago by • 0
0
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1
reply
758
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DESeq2 gives an error and R crashes
DESeq2
20 months ago • updated 19 months ago Shefali • 0
0
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2
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824
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 20 months ago by 43k • written 20 months ago by ▴ 70
0
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1
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846
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 20 months ago by 43k • written 20 months ago by • 0
0
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2
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766
views
Regressing out batch effects
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
0
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2
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1.0k
views
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
1
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1
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843
views
DESeq2 - Missing values in count matrix
DESeq2
updated 20 months ago by 68k • written 20 months ago by • 0
1
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6
replies
1.6k
views
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
reply
513
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
20 months ago Layal • 0
0
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2
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737
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
20 months ago michelafrancesconi8 • 0
0
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4
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1.1k
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
0
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1
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443
views
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
2
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4
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1.4k
views
PCA of different bacterial species
DESeq2
written 20 months ago by ▴ 10
0
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1
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606
views
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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778
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
20 months ago Anita ▴ 10
1
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2
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885
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
20 months ago Chanderkant Chaudhary • 0
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2
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2.0k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
20 months ago kcarey • 0
2
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3
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835
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 20 months ago by 43k • written 20 months ago by ▴ 20
0
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3
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944
views
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
reply
708
views
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
reply
447
views
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
4,840 results • Page 6 of 97
Recent ...
Replies
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
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
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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