Showing : rnaseqdata • reset
6
votes
4
replies
10k
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How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 2.3 years ago by • 0 • written 3.1 years ago by ▴ 10
2
votes
6
replies
8.6k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
2.1 years ago treebig44 ▴ 30
22
votes
15
replies
7.3k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 5 months ago by ▴ 10 • written 2.0 years ago by ▴ 50
0
votes
3
replies
7.3k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
8
votes
2
replies
6.7k
views
handling outliers with DESeq2
RNASeqData DESeq2 Outliers
3.0 years ago paty ▴ 60
7
votes
5
replies
3.3k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
3.4 years ago ecg1g15 ▴ 20
0
votes
10
replies
2.8k
views
GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer RNAseqData GenomicFeatures Cancer RNAseqData GenomicFeatures
updated 9.8 years ago by ▴ 320 • written 9.8 years ago by ★ 6.8k
2
votes
4
replies
2.8k
views
Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
3.4 years ago ecg1g15 ▴ 20
1
vote
2
replies
2.4k
views
Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 19 months ago by ★ 1.3k • written 19 months ago by • 0
1
vote
15
replies
2.4k
views
between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
3.0 years ago demisa • 0
4
votes
1
reply
2.3k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 2.1 years ago by 41k • written 2.1 years ago by ▴ 30
2
votes
8
replies
2.3k
views
While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 3.0 years ago by 50k • written 3.0 years ago by ▴ 20
2
votes
9
replies
2.2k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
22 months ago Peipei • 0
0
votes
5
replies
2.1k
views
Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
24 months ago • updated 22 months ago priyanka.m • 0
1
vote
1
reply
2.1k
views
Limma interaction term
RNASeqData limma DifferentialExpression
updated 2.1 years ago by 50k • written 2.1 years ago by • 0
1
vote
3
replies
1.7k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
3.0 years ago dantasezequiel1 • 0
1
vote
7
replies
1.6k
views
DESeqDataSetFromMatrix error
BiocGenerics DESeq2 DEGreport RNASeqData DEG
updated 21 months ago by 65k • written 21 months ago by • 0
1
vote
2
replies
1.5k
views
Binning expression data along with capturing gene identifiers
rnaseqdata clustering
updated 9.2 years ago by ★ 2.0k • written 9.2 years ago by ▴ 150
1
vote
2
replies
1.4k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 8 months ago by ▴ 120 • written 8 months ago by ▴ 10
0
votes
2
replies
1.3k
views
How to run vst transformation
RNASeqData vst
updated 23 months ago by 41k • written 23 months ago by • 0
3
votes
3
replies
1.3k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
22 months ago JK Kim ▴ 20
2
votes
3
replies
1.3k
views
RNA-seq analysis without replicates
DESeq2 RESEQ RNASeqData
updated 12 months ago by • 0 • written 12 months ago by • 0
1
vote
6
replies
1.3k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
3.2 years ago Seaweed • 0
3
votes
4
replies
1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.0 years ago hgalmoore • 0
2
votes
5
replies
1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 13 months ago by • 0
0
votes
1
reply
1.3k
views
'Negative' and 'Positive' bigWig RNAseq files: how to deal with these???
bigWig RNASeqData
2.2 years ago bas_work ▴ 30
3
votes
6
replies
1.3k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 3.4 years ago by 41k • written 3.4 years ago by ▴ 50
1
vote
4
replies
1.2k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2 Log2FC RNASeqData
15 months ago Iwan • 0
1
vote
5
replies
1.2k
views
Error in DEseq
DEseq RNASeqData
updated 22 months ago by ★ 4.0k • written 22 months ago by • 0
2
votes
3
replies
1.2k
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
23 months ago Maka • 0
4
votes
3
replies
1.2k
views
Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 2.1 years ago by ★ 1.3k • written 2.2 years ago by ▴ 10
0
votes
6
replies
1.2k
views
while doing co-expression network analysis, I am getting an error
RNASeqData
3.0 years ago Rishav ▴ 20
2
votes
4
replies
1.1k
views
DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
2.6 years ago khaveh ▴ 10
0
votes
2
replies
1.1k
views
lncRNA Genes in a Dataset
ncRNAtools RNASeqData
2.0 years ago sushimoto • 0
3
votes
3
replies
1.1k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
7 months ago • updated 6 months ago Ethan Nguyen • 0
1
vote
1
reply
1.1k
views
Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 2.5 years ago by 50k • written 2.5 years ago by • 0
0
votes
2
replies
1.1k
views
Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
RNASeqData DESeq2
updated 2.0 years ago by 41k • written 2.0 years ago by ▴ 30
2
votes
3
replies
1.1k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
2
votes
4
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 4 months ago by • 0 • written 10 months ago by • 0
0
votes
1
reply
1.0k
views
RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2 multiple factor design rnaseqdata
updated 8.0 years ago by 41k • written 8.0 years ago by ▴ 80
0
votes
4
replies
1.0k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
11 months ago ruba-mahmoud • 0
1
vote
4
replies
1.0k
views
lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
2.0 years ago sushimoto • 0
2
votes
3
replies
1.0k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 8 months ago by 65k • written 8 months ago by ▴ 10
0
votes
2
replies
977
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
3
replies
941
views
Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 2.9 years ago by ★ 1.3k • written 2.9 years ago by • 0
3
votes
2
replies
917
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.0 years ago • updated 23 months ago Dakarai ▴ 10
3
votes
2
replies
914
views
Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
3.1 years ago Wuschel ▴ 10
3
votes
3
replies
876
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
9 months ago amnahsiddiqa ▴ 10
0
votes
0
replies
849
views
high number of reads mapped to too many loci
RNASeqData
2.1 years ago vasa.broz • 0
50 results • Page 1 of 1
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Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, this is the MDS plot at genes level. I don't have the raw data but I think the normalized data. So can we say from the plot that…
Comment: How to correct for known and surrogate variables in DESeq2? by Michael Love 41k
To question 3: if you model technical variation using only ~group vs ~1, then it will be correlated with known technical variables, which y…
Answer: flowStats Search Error by shepherl 3.8k
We are aware of an issue with bioconductor.org search and are investigating. We apologize for an inconvenience this is causing.
Comment: How to correct for known and surrogate variables in DESeq2? by nhaus ▴ 30
Hey Crystal, did you end up getting advice? I am facing the exact same questions that you are having right now. Would be very grateful if y…
Answer: List of Deprecated Packages for Bioc3.18 by shepherl 3.8k
previously unannounced, COHCAP is not deprecated but removed with release 3.19. see [mailing list discussion](https://stat.ethz.ch/piperm…
Votes
C: Add new columns to DESeqResults from text file by matching rownames.
Answer: geneList error in clusterprofiler
Comment: Memory errors using read.bismark?
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
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