Showing : DeSeq2 • reset
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Do we need to correct any of the data from DESeq2, if we only want to investigate some of the comparisons?
DESeq2 correction
3.2 years ago smac_head • 0
0
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3
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2.3k
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Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
2
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2
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1.3k
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Gene abundance DESEq
DESeq2
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
1
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3
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1.9k
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Clarification about DESeq2 counts() function when dealing with covariates
DESeq2
updated 3.2 years ago by ★ 1.4k • written 3.2 years ago by • 0
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5
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6.4k
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DESeq2 is not available for R version 4.2.1
DESeq2
3.2 years ago annamariabugaj ▴ 10
1
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2
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5.3k
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Getting the normalized counts after running DESeq()
DESeq2 Normalization
updated 3.2 years ago by ▴ 10 • written 3.2 years ago by • 0
1
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2
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1.2k
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DESEQ2 Normalisation Factor
DESeq2
3.2 years ago MAHESH • 0
0
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1
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850
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DESeq2 : LRT with factorial and continuous data
DESeq2 DifferentialExpression
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
1
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6
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5.9k
views
Weird looking volcano plot
DESeq2 volcano
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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1
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932
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Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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2
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723
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DESeq2 with incorrect adjusted Pvalues
DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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2
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1.1k
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Overwhelmed by DESEq2 options and how to answer my questions.: Two conditions and Three families
DESeq2
3.2 years ago lgspeight • 0
1
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3
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1.6k
views
different stat and p values when filtering or not by lfc in DESeq2
DESeq2 wald stat
updated 3.2 years ago by ▴ 760 • written 3.2 years ago by • 0
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3
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1.1k
views
code syntax for DESeq2 to derive DEGs from a complicated contrast or interaction contrast?
DESeq2 Complicated.contrast DEGs
updated 3.2 years ago by 43k • written 3.2 years ago by • -60
1
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1
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1.2k
views
What is the effect of passage number in the differential gene expression when performing RNA sequencing analysis?
DESeq2 passagenumber
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
1
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1
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882
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
0
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2
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2.2k
views
clarification of the way of converting standard error to confidence interval for logFC in DESeq2 result table
DESeq2 Confidence.Interval
3.2 years ago Mike • -60
0
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1
reply
687
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ref treatment
DESeq2
updated 3.2 years ago by ★ 1.4k • written 3.2 years ago by • 0
2
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1
reply
995
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Time-series analyses of a multifactor design with DESeq2
DESeq2 MultipleFactors TimeSeriesExperiment
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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4
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2.5k
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DESeq2 lfcThreshold - all my padj are equal to 1
DESeq2 lfcThreshold
3.3 years ago • updated 3.2 years ago Abir.khazaal ▴ 10
3
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2
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5.4k
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Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by • 0
5
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6
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2.6k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 3.2 years ago by 53k • written 3.3 years ago by • 0
0
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2
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2.1k
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output file conversion from FeatureCount to DESeq2 - no duplicate for samples
DESeq2 FeatureCount
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
2
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3
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2.3k
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DESeq2 contrasts using all relevant samples vs all samples
DESeq2
3.3 years ago jeffrey.maurer • 0
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7
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2.7k
views
DESeq2 Error in checkContrast(contrast, resNames) : when using list()
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
5
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1
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908
views
Log2FC values slightly higher in some genes after DESeq2 shrinkage
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
1
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3
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1.8k
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resultsNames(dds) not showing all contrasts
DESeq2 resultsNames lfcShrink
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
1
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5
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2.3k
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DESeq2 - Replacing outliers with continuous variable in design
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
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5
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2.4k
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DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 6 months ago by 43k • written 3.3 years ago by • 0
0
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3
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1.4k
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Time course RNA seq with DESeq2
DESeq2
updated 3.3 years ago by ▴ 10 • written 3.3 years ago by • 0
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1
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758
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DESeq2 analysis with 3 factors
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
2
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1
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1.1k
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How to make the data compatible for DESeq2?
DESeq2 TPM rawcounts StringTie
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 200
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1
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918
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DESeq2 Design Matrix
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 20
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4
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1.2k
views
DESeq2 likehood ratio
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
0
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1
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697
views
DESeq2 likehood ratio
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
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1
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1.8k
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Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
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3
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1.7k
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DESEq2 rerun gives different results
DESeq2
3.3 years ago Mia • 0
4
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5
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4.2k
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Importance of Order in Design Formula
deseq2
updated 3.3 years ago by • 0 • written 6.4 years ago by • 0
1
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2
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800
views
how to plot the union of the 100 most expressed genes
DESeq2 RNASEQ
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
0
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1
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606
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DESeq2 comparison of different sample combinations
DESeq2
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by • 0
1
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1
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1.1k
views
DESeq 2 failes to load
Bioconductor DESeq2
3.3 years ago Ruggero ▴ 10
2
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2
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1.1k
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data import error
DESeq2
3.3 years ago sumitra • 0
0
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2
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1.7k
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DESeq2 on normalized data
DESeq2
3.3 years ago lizaaa • 0
0
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1
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807
views
Differentially expressed genes from Deseq2 have similar counts
DESeq2
updated 3.3 years ago by ▴ 780 • written 3.3 years ago by • 0
0
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1
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651
views
Batch correction in deseq2
DESeq2
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by ▴ 40
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1
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1.5k
views
Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System
RNASeq Correlation DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
1
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3
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1.9k
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Strange Dispersion plot
DESeq2
3.3 years ago Yiqi ▴ 10
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1
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1.0k
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Correlation between CpG methylation and gene expression from DESeq2-> Normalization of counts using VST + fpkm/rpkm for optimal normalization?
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
1
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4
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9.4k
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TPM normalization starting with read counts
edgeR DESeq2
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
0
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1
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911
views
DESeq errpr in normalizePath
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
4,840 results • Page 19 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
Upcoming Ensembl API and data access changes - new blog post available
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
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