Showing : DESEQ2 • reset
3
votes
4
replies
4.4k
views
Deseq2's geometric mean calculation and 0s
deseq2 normalization
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 10
0
votes
2
replies
838
views
Custom dispersion estimate DESeq2
deseq2 edger
updated 5.2 years ago by ★ 29k • written 5.2 years ago by ▴ 110
3
votes
7
replies
7.2k
views
limma::removeBatchEffect into DESeq2
deseq2 limma batch effect
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by • 0
1
vote
4
replies
2.5k
views
Issues with DESeq2 LRT for time-course experiment
rna-seq R DESeq2 LRT
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 10
2
votes
5
replies
1.8k
views
stat value is throwed out after lfcShrink in DESeq2
deseq2
updated 15 months ago by 43k • written 5.2 years ago by ▴ 40
18
votes
4
replies
43k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 5.2 years ago by ▴ 220 • written 5.2 years ago by ▴ 10
2
votes
7
replies
2.1k
views
can the counts extracted from Diffbind be used to analysis in Deseq2 as the RNAseq?
deseq2 diffbind
updated 3.5 years ago by ★ 5.2k • written 5.2 years ago by ▴ 10
8
votes
16
replies
6.9k
views
Transcript-level differential expression using DESeq2
deseq2 transcript-level differential expression
updated 3.5 years ago by • 0 • written 5.2 years ago by ▴ 20
17
votes
13
replies
22k
views
deseq2 normalized data with heatmap
deseq2
updated 4.4 years ago by ▴ 10 • written 5.2 years ago by ▴ 20
0
votes
5
replies
1.2k
views
DESeq2 reporting >10,000 DEGs
deseq2
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
5
votes
4
replies
2.5k
views
how to understand DESeq2 results comparison
deseq2
updated 5.2 years ago by ★ 1.4k • written 5.2 years ago by ▴ 20
4
votes
5
replies
4.2k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
2
votes
8
replies
6.0k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
5.3 years ago Pietro ▴ 40
2
votes
5
replies
1.5k
views
the results from normalized=TRUE and normalized = FALSE is the same
R deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
0
votes
5
replies
1.2k
views
Testing effect of multiple continuous variables using DESeq2
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
3
replies
1.1k
views
Error using DESeq2's nbinomLRT
deseq2 LRT
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 30
6
votes
4
replies
4.0k
views
Having TMM for GSEA
edger deseq2
updated 4.7 years ago by ★ 4.0k • written 5.3 years ago by ▴ 30
0
votes
2
replies
812
views
Problems regarding DESeq2 package installation in R
deseq2
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
1
vote
2
replies
761
views
Unexpected rlog values when count spread is large
deseq2 normalization
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
1
reply
1.1k
views
Differential expression analysis comparison using more that two variables
deseq2 Tutorial
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
2
votes
8
replies
2.8k
views
Differential gene expression using R
deseq2 edger normalization limma
updated 5.3 years ago by 53k • written 5.3 years ago by • 0
1
vote
4
replies
2.5k
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2 apeglm rna-seq spike-in
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
0
votes
1
reply
1.1k
views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2 LRT RNAseq condition
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 30
3
votes
2
replies
2.9k
views
lfcShrink function in DEseq2 and s-values
deseq2 apeglm
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
3
votes
3
replies
1.1k
views
droplevels not working - error in DESeq() function
deseq2
5.3 years ago DcL-A • 0
1
vote
3
replies
866
views
Normalizing counts for cross-species correlation test
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
3
votes
2
replies
1.8k
views
Variance stabilized values and batch correction
deseq2 vst
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
0
votes
1
reply
474
views
DESeq2 differentially expressed genes
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
7
votes
8
replies
2.9k
views
Cook's Distance Outliers: None reported in results table and "cooksCutoff" modification has no effect
deseq2 outliers cooks cooks distance
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
vote
1
reply
1.0k
views
Can I add raw counts for duplicated genes?
DESeq2 RNAseq
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
12
replies
3.1k
views
Error Message in DESEQ (DESEQDataSetFromMatrix)
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
2
votes
2
replies
1.7k
views
Time series RNA-Seq data analysis using DESEQ2
deseq2
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 10
0
votes
1
reply
730
views
Missing Point in PCA Analysis
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
votes
2
replies
1.5k
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
0
votes
1
reply
690
views
Obtaining expanded model matrices when using apeglm
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
0
votes
10
replies
1.5k
views
Deseq2 nested LRT analysis
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
1
vote
2
replies
9.0k
views
DESeq2 normalization and TPM
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 100
0
votes
1
reply
401
views
Normalising allele-specific reads from RNA seq
deseq2
5.3 years ago chandel12oct • 0
8
votes
5
replies
8.5k
views
Understanding interaction term in DESeq2
deseq2 design formula log fold change
updated 15 months ago by 43k • written 5.3 years ago by ▴ 40
1
vote
1
reply
1.2k
views
Error in importing Salmon quantification to R using tximeta
deseq2 tximeta
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
1
vote
1
reply
958
views
Error in importing Salmon quantifications into R with tximport
deseq2 tximport
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
3
votes
7
replies
1.8k
views
DESeq2 Interspecies comparisons
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
1
reply
533
views
Paired samples in design including 2 conditions and 4 drug dosages
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
votes
3
replies
1.5k
views
Differential gene expression using DESeq2 on Ribo-Seq data
DESeq2 Ribo-Seq differential gene expression
5.3 years ago DataFanatic ▴ 10
0
votes
1
reply
1.7k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
votes
1
reply
2.0k
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
0
votes
3
replies
1.7k
views
dealing with BATCH effect/ donor variation in RNA seq data
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
vote
9
replies
4.7k
views
DESeq: Error in model.matrix.formula(design(object), data = colData(object)) : data must be a data.frame
deseq2
updated 5.3 years ago by ▴ 10 • written 9.7 years ago by ▴ 10
1
vote
6
replies
1.5k
views
DESeq2 size factors change with fixed geometric means
size factors deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
vote
3
replies
2.3k
views
unable to install DESeq2 there is no package called XML
deseq2 bioconductor windows xml installation
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
4,839 results • Page 37 of 97
Recent ...
Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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