Showing : DEseq2 • reset
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Design formula in DeSeq2 to control for a variable
deseq2
updated 4.9 years ago by 43k • written 7.4 years ago by • 0
1
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4
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1.8k
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Analysis Time course data using DESeq2
deseq2 timecourse multiple time points time-series
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
1
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2
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1.1k
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some questions about using the rlog function of DEseq2
deseq2 rna-seq
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
5
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9
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6.2k
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remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
deseq2 rnaseq
updated 7.4 years ago by ▴ 10 • written 10.6 years ago by ▴ 70
2
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2
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528
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DESeq2 Ignore Some Significant Differential Genes due to Extreme Count Outlier
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
1
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5
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1.6k
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Differential analysis based on selection of random samples
r differential gene expression deseq2 bioconductor rnaseq
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 60
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3
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1.3k
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3x2 comparisons in DEseq - time (3 time points) and two treatments
deseq2 deseq rna-seq multiple comparisons
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 60
1
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1
reply
1.3k
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DeSeq2 independant filtering barely removes any genes
deseq2 differential gene expression filtering
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
2
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4
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8.0k
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Understanding Contrasts when analyzing DESeq2 results
deseq2 extracting contrasts rnaseq interaction term
updated 7.4 years ago by ★ 1.4k • written 7.4 years ago by ▴ 10
0
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3
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1.4k
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A contrast with four simultaneous conditions for DESeq2?
DESeq2 contrast results
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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4
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1.8k
views
Error in Apeglm Method for Effect Size Shrinkage
deseq2 apeglm
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 50
3
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3
replies
2.1k
views
Have I used Deseq2 ,on protein array data, correctly? Or should I be using another R package
r deseq2 protein microarray
updated 7.4 years ago by 53k • written 7.4 years ago by • 0
0
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1
reply
1.0k
views
Deseq2 within samples variability
within variability samples deseq2
updated 7.4 years ago by 43k • written 7.5 years ago by • 0
1
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2
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2.7k
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DESeq2 Design matrix - Time series, treatment, and individual
deseq2
7.4 years ago jg1989 • 0
2
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3
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2.1k
views
DESeq2 for time series using time as continuous and looking at effect of time on DE
deseq2 timecourse multiple time points mlr michael love
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
1
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3
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9.4k
views
could not find function "DESeqDataSetFromMatrix
deseq2
updated 7.4 years ago by ★ 1.1k • written 7.4 years ago by • 0
0
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1
reply
554
views
Question about DESeq2 design
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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4
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2.1k
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Deseq2 problem visualizing gene expression with batch corrected values
deseq2 limma differential expression visualization
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
1
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4
replies
1.7k
views
DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
deseq2 sequence length normalization RSEM tximport differential expression
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 50
3
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3
replies
1.9k
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DESseq2: Why can the dispersion be generelized over the conditions?
deseq2 dispersion estimatedispersions
updated 7.4 years ago by ★ 7.9k • written 7.4 years ago by ▴ 20
1
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7
replies
3.1k
views
Visualization for Time Course "LRT" test in DESeq2
deseq2 time-course
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 50
3
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12
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6.0k
views
The calculation of regularized logarithm
rnaseq deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 20
0
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6
replies
1.6k
views
DESeq2 - how to build design for matched case-control study with repeated measurement
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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1
reply
646
views
2x2 design - UP means more expression on S than R and DOWN less expression on S than R?
deseq2 2x2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
4
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4
replies
3.8k
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DESeq2 for Ribosomal profiling analysis [two-factor designs]
deseq2 ribosome profiling
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
0
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5
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1.9k
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DESEQ2 Default Value for Cooks Distance cutoff
deseq2
updated 10 months ago by 43k • written 7.4 years ago by • 0
4
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6
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4.5k
views
Get release date for version of DESeq2
deseq2 r
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 20
3
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7
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2.1k
views
Compare effect size of gene (lfcShrink or not)
deseq2 rnaseq
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 20
1
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5
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3.2k
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DESeq2 Subsetting gives error in contrasts - can be applied only to factors with 2 or more levels
deseq2 multiple factor design contrast
7.5 years ago russell.stewart.j • 0
1
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1
reply
2.3k
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non-integer counts in DESeq2
deseq2 differential gene expression
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
1
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2
replies
909
views
DESeq2 significative fold change when both groups have no reads
deseq2
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 170
1
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2
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2.4k
views
very different DESeq2 results between two versions
deseq2 rnaseq
7.5 years ago sven.schenk ▴ 30
0
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1
reply
1.3k
views
Model matrix not full rank
DESeq2 model matrix not full rank batch effect
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
2
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2
replies
5.2k
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Interpreting results of sample-to-sample PCA/clustering and changing assignment of condition levels
deseq2 DESeq2
7.5 years ago fl ▴ 20
0
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4
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1.5k
views
Is circular RNA read out as linear fragments during Rsubread-DESeq2
deseq2 circrna rsubread
updated 7.5 years ago by ★ 3.6k • written 7.5 years ago by • 0
6
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3
replies
4.7k
views
ntop parameter in plotPCA(). DESeq2
deseq2
updated 4.3 years ago by 43k • written 7.5 years ago by ▴ 40
0
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1
reply
897
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Bad replicate DESeq2
deseq2
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 100
0
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1
reply
2.3k
views
DSEq2 error message at loading
deseq2
updated 7.5 years ago by ★ 1.1k • written 7.5 years ago by • 0
0
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3
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2.4k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
0
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4
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5.4k
views
DESeq2 library loading error
deseq2
updated 4.7 years ago by 43k • written 7.5 years ago by • 0
1
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2
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1.6k
views
Whether "read_counts_miRNA" or "reads_per_million_miRNA" to use for DE expression analysis using DeSeq2
tcgadownload deseq2 mirna normalization
updated 7.5 years ago by ▴ 140 • written 7.5 years ago by • 0
1
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2
replies
699
views
Differential expression across time points
deseq2
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
0
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2
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1.5k
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Error in DESeq2 Unmix() function: L-BFGS-B needs finite values of 'fn'
deseq2 biocViews
7.5 years ago • updated 12 months ago JennyS • 0
0
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6
replies
2.1k
views
Defining subsets for FDR correction
fdr deseq2 ihw
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 30
4
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4
replies
3.2k
views
Applying varianceStabilizingTransformation to log transformed RNA seq data from cBioPortal
variancestabilizingtransformation rnaseq cBioPortal deseq2
updated 7.5 years ago by ▴ 20 • written 7.5 years ago by • 0
4
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4
replies
2.3k
views
What doest this p.value distribution mean?
deseq2 pvalue
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
0
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1
reply
931
views
How to get normalized counts and do differential expression using time series data (gene knock down) using DESeq2
deseq2
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
0
votes
7
replies
1.3k
views
DeSeq2 Question - Reading Sample Table to DESeqDataSet
deseq2
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
2
votes
5
replies
2.3k
views
rlog, lfcShrink and vst on gene subset
deseq2 subsetting plot
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 10
0
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1
reply
1.2k
views
2 factors interaction with Deseq2
deseq2
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
4,840 results • Page 62 of 97
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Replies
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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Popular Question to shepherl 4.2k
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