Showing : DEseq2 • reset
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problem DESeq2 paired samples analysis
deseq2
7.7 years ago zhizhon • 0
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2
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Issues installing packages miniconda environment
bioclite deseq2 miniconda packages
7.7 years ago cpat • 0
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12
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2.2k
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DESeq2 multifactor design with interaction term
deseq2 multiple factor design interaction term
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
4
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12
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2.6k
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Incredibly high/low foldChange
deseq2
7.8 years ago • updated 7.7 years ago jovel_juan ▴ 30
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3
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2.1k
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RNA-seq: Time-course data normalisation with TPM
rna-seq normalization deseq2 TPM
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 10
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2
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1.3k
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Interpretation of results names after LRT
DESeq2 LRT multiple time points
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 60
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5
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1.8k
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results {DESeq2} parameters
deseq2 results
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 20
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1.3k
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Removal of outliers after library size correction, can I save this to my dds object?
deseq2 outliers
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
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1
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1.9k
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DESeq2 question about predicting abundance adjusted for covariates.
deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
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3
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2.3k
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choose between normalization techniques for OTU counts
deseq2 normalization R edger
7.8 years ago • updated 7.7 years ago apfelbapfel ▴ 30
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6
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2.2k
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DESeq2 It is correct to use interaction term for patient variability?
deseq2 design interaction term R
written 7.8 years ago by • 0
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2
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3.4k
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use tximport's countsFromAbundance when using DESeq2
deseq2 tximport normalization salmon rnaseq
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
7
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4
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4.0k
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Normalized counts of DESeq2 affected by design formula?
deseq2
updated 23 months ago by • 0 • written 7.7 years ago by ▴ 20
0
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1
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1.6k
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Best way to analyze multiple treatments using DESeq2?
deseq2 rna-seq mirna
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
1
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1
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1.6k
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DESeq, DESeq2 or EdgeR normalization for gene expression on multiple tissues without replicates ?
normalization deseq2 edger
updated 7.8 years ago by ★ 29k • written 7.8 years ago by ▴ 10
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2
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1.2k
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Does "FRY gene set tests" is possible using a DESEQ2 style analysis ?
deseq2 fry gene tests
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 20
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6
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2.1k
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weird behaviour DESeq2 1.18.1
deseq2 outliers version
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 90
1
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3
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1.5k
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plotMA (DESeq2) Issue
deseq2 plotMA rnaseq logfoldchange
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
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651
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Does DeSeq2 normalizes for high sample variance between biological replicates?
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
4
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4
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3.2k
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Using DADA2 output for DESeq2
deseq2 dada2
updated 7.8 years ago by ▴ 50 • written 7.8 years ago by ▴ 20
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1
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1.3k
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Changing group labels yields different results in DESeq2
deseq2 multiple groups
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
1
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3
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1.1k
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very low number in normalized count but give very high in log2foldchange
deseq2
7.8 years ago naktang1 • 0
0
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3
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2.1k
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Error in DESeq "object" not found
deseq2 LRT reduced model
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 60
8
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2
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11k
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DESeq2 analysis with only two replicates
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 30
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11
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2.8k
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Strange dispersion plot
deseq2 dispersion
7.8 years ago Moose123 • 0
0
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4
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3.8k
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DESeq2 - DESeqDatasetFromMatrix
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
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2
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977
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Re-calculate DESeq from dds based on another design
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 20
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2
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942
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find gene only express in one condition in Deseq2
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
1
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5
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2.4k
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To analyze the overall variance, which one to choose, vst or DESeq2 normalized counts?
deseq2
updated 7.8 years ago by ▴ 20 • written 7.8 years ago by ▴ 20
1
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2
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2.7k
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DESeq2 - MAP and MLE - log2FoldChange
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
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1
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536
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DESeq2 package - different results
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
2
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1
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1.1k
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DESeq2-No replicates-Utility of log2fold shrunk values?
deseq2 rnaseq
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
1
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8
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2.1k
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design versus interaction term similarities and/or differences?
deseq2 ANOVA design interaction term
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
1
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2
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2.1k
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lfcShrink: Error when using numerical contrast vector
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
2
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1
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5.5k
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Using DESeq2 to analyse TCGA data
deseq2 tcga tcgabiolinks gene expression differential expression
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
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8
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6.6k
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Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
7.8 years ago Marina ▴ 40
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5
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2.0k
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How to set up the Wald test testing for log2 fold change above a threshold, and interpret the result correctly?
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 20
3
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16
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3.1k
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DESeq2 interaction term
DESeq2
7.8 years ago Catalina Aguilar Hurtado ▴ 90
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5
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1.1k
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Different version of DESeq2
deseq2 mikelove
7.8 years ago marika.catapano • 0
6
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7
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6.4k
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Is it reasonable to run DESeq2 on only a subset of transcripts of the original raw count matrix?
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 20
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4
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2.1k
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DESeq2 for Time course experiments
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 10
0
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10
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1.6k
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DESEQ2 Grouping vs interaction and dds
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 20
0
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2
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4.5k
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DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2 goseq rnaseq go enrichment differential gene expression
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
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2
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1.7k
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Filtering genes with a minimum number of counts between samples
DESeq2 filtering
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 60
0
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4
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1.1k
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Using a truth table for ColumnData in DESeq2
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 10
0
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4
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1.8k
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Normalise counts when tumour samples have normal tissue contamination.
deseq2 deseq edgeR rnaseq htseqcounts
7.8 years ago Deepali • 0
0
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2
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2.7k
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Deseq2 raw counts input as integers
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 90
1
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2
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3.3k
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DESeq2 plotCounts() function-what is the unit on y axis?
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 20
2
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3
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1.2k
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DESeq2 using multiple conditions
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 20
0
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4
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2.4k
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Deseq2 padj value very low
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 40
4,840 results • Page 66 of 97
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Comment: 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
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.
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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