Showing : DEseq2 • reset
3
votes
8
replies
2.0k
views
Filtering for genes >100 counts after LRT still showing significant genes with genes with 0 counts!
LRT CPM lowcountgenes deseq2
7.8 years ago A ▴ 60
4
votes
1
reply
3.2k
views
DeSeq2 with three groups which approach to use? LRT or just do multiple pairwise comparisons?
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 170
0
votes
7
replies
1.2k
views
Identifying significantly differentially expressed genes across all the groups within a factor using DESeq2
deseq2
updated 7.8 years ago by • 0 • written 7.8 years ago by • 0
5
votes
4
replies
4.3k
views
DESeq2 taking long time to run with 270 samples in 10 groups.
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 40
2
votes
4
replies
1.9k
views
Standard error of log2FC from DESeq in time series experiment
deseq2 log2fc standard error timecourse
updated 7.8 years ago by • 0 • written 7.8 years ago by • 0
1
vote
2
replies
1.2k
views
DESeq2 lfcShrink time for analysis
deseq2 lfcshrink
updated 7.8 years ago by • 0 • written 7.8 years ago by ▴ 10
0
votes
11
replies
2.1k
views
LFC shrinkage executed when not expected (DESeq2)
deseq2
7.8 years ago Jonas B. ▴ 40
0
votes
1
reply
1.9k
views
MA plot interpretation .
MAPLOT DESEQ2 RNASEQ
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
votes
1
reply
845
views
testing interaction with 3 factors in DESEq2
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
votes
4
replies
1.9k
views
significant genes with DESeq2 plenty of outliers and zero counts
zero counts deseq2 odd results outliers
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 90
2
votes
4
replies
1.7k
views
X-axis of MAplot and lfcShrink
deseq2
8.1 years ago • updated 7.8 years ago Yuya Liang ▴ 20
1
vote
5
replies
1.5k
views
compare one group to mean of two others in DESeq2 with betaprior=FALSE
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 40
1
vote
9
replies
1.4k
views
Compare more than one factor
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 20
0
votes
4
replies
3.0k
views
Problem converting first column to rownames
deseq2 countdata
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 60
4
votes
7
replies
3.7k
views
DESeq2 vs TCGAbiolinks normalization methods
normalization rnaseq deseq2
updated 4.0 years ago by • 0 • written 7.8 years ago by ▴ 420
1
vote
3
replies
1.6k
views
Normalization / size factors of samples with high expression of few genes (viral infection)
deseq2 normalization sizefactors
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 40
0
votes
1
reply
1.8k
views
DESeq2: same count matrix, different design
deseq2 baseMean cooks distance
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 30
2
votes
1
reply
1.6k
views
DESeq2: multiple genotypes time course
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 10
1
vote
2
replies
741
views
Running DESeq2 for different types of data
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
1
vote
4
replies
1.0k
views
Pairwise Comparison between A Large Number of Groups
deseq2 differential gene expression
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
votes
3
replies
1.4k
views
Is this procedure necessary in DESeq2 for my data
deseq2 multiple factor design nested design
7.8 years ago michael.steffen ▴ 20
0
votes
6
replies
8.1k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
deseq2 R genomics
7.8 years ago mokunf • 0
3
votes
4
replies
3.4k
views
DESeq2 batch effect modeling and matrix not full rank
deseq2 rnaseq rna-seq
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 20
19
votes
7
replies
15k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2 ensembl
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 170
0
votes
4
replies
1.3k
views
can DESeq2 be used to compare these miRNA read counts from 9 samples?
deseq2 rnaseq
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
8
votes
3
replies
6.0k
views
DESeq2 with interaction using SVA
deseq2 sva interaction term grouping variable deseq
7.8 years ago kevin.kingsland ▴ 70
6
votes
4
replies
6.2k
views
Are two biological replicates enough for a transcriptome analysis using DESeq2?
deseq2
updated 7.8 years ago by 21k • written 7.8 years ago by ▴ 40
4
votes
6
replies
2.2k
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 60
1
vote
7
replies
2.6k
views
Low Counts in top DE genes in DESeq2
deseq2
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 70
0
votes
4
replies
2.7k
views
rlog transformation producing outliers with very high log-transformed counts
deseq2 rlog
7.8 years ago Frederik Ziebell ▴ 30
4
votes
4
replies
1.6k
views
what the first row without a gene name?
deseq2
updated 4.8 years ago by 68k • written 7.8 years ago by ▴ 20
0
votes
0
replies
1.4k
views
How to call "DBA_CONDITION" for mutiple conditions and How to control GLM program
cancer deseq2 edger CONDITIONS DBA
7.8 years ago arcucamila • 0
0
votes
3
replies
1.4k
views
DESeq2 Model matrix not full rank error despite fully-crossed experimental design
deseq2 multiple factor design
updated 7.8 years ago by 43k • written 7.9 years ago by • 0
0
votes
2
replies
1.4k
views
Installing DEseq packeges under windows10 , can't find library after succesful install
deseq2 package installation
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
2
votes
4
replies
6.6k
views
Age covariate continuous vs. categorical
deseq2 linear model covariates age design model
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
1
vote
6
replies
2.1k
views
how to analysis htseq-count
deseq2
written 7.9 years ago by ▴ 30
1
vote
2
replies
4.2k
views
Applying SVA to RNA-Seq dataset
DESeq2 sva svaseq batch effect correction
7.9 years ago L_K • 0
2
votes
1
reply
2.7k
views
Error in DESeq2 plotMA from object subset
deseq2 maplot subset
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 60
1
vote
2
replies
1.9k
views
DESeq2 design & model matrix not full rank - am I nesting correctly?
deseq2 model matrix experimental design multiple factor design
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
votes
1
reply
3.7k
views
DESeq2 design model/contrasts question 3 level condition
deseq2 model design differential gene expression experimental design
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
votes
2
replies
1.2k
views
DESeq2, no significantly DE genes
deseq2 differential expression adjusted pvalue
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 60
1
vote
1
reply
1.0k
views
Nested design with unbalanced groups
deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
votes
1
reply
4.5k
views
DESeq2 contrast with list no longer works: all elements of the contrast as a list of length 2 should be elements of 'resultsNames(object)'
deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
1
vote
7
replies
3.0k
views
DESeq2 experimental design, 2 controls and 2 treated
Deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
0
votes
1
reply
1.7k
views
Handling outliers in Deseq2
outliers deseq2 logfoldchange
7.9 years ago lirongrossmann ▴ 80
0
votes
2
replies
1.5k
views
Differential analysis between single sample vs single sample (control vs treatment) with no replicates
r bioconductor limma edger deseq2
updated 7.9 years ago by ★ 29k • written 7.9 years ago by ▴ 120
2
votes
3
replies
1.9k
views
GRanges object from gene list
granges bed genomicranges genomeintervals deseq2
7.9 years ago rbronste ▴ 60
1
vote
1
reply
2.3k
views
sample removal after clustering
deseq2 rlog transformation
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
votes
1
reply
4.9k
views
DESeq2 - How to study time course experiment taking subject variability into account?
deseq2 repeated measures time course
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
votes
1
reply
1.7k
views
Data object format for deseq2
deseq2 R RSEM
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
4,840 results • Page 67 of 97
Recent ...
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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