Showing : RNAseq • reset
6
votes
5
replies
4.0k
views
VST for scRNA-seq
deseq2 rnaseq normalization
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 50
0
votes
4
replies
2.1k
views
coseq plotting error: no method for coercing this S4 class to a vector
coseq RNAseq clustering
updated 5.7 years ago by ▴ 80 • written 5.7 years ago by ▴ 40
2
votes
4
replies
3.0k
views
edgeR design matrix and contrasts for comparisons both between and within subjects
edger rnaseq design and contrast matrix
updated 5.7 years ago by 53k • written 5.7 years ago by • 0
0
votes
0
replies
1.5k
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
5.7 years ago jam526 • 0
1
vote
2
replies
1.3k
views
Time series experiment analysis in DEseq2 without T=0 and three independent experiments with linked samples
deseq2 rnaseq repeated measures time series design formula
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 10
0
votes
3
replies
1.0k
views
Cannot figure out why the DE genes' FDR > 0.05 in edgeR output
edger rnaseq
updated 5.7 years ago by 53k • written 5.7 years ago by • 0
0
votes
1
reply
1.8k
views
plot statistic values in a DEseq2 plotCounts plot
deseq2 plotCounts pvalues RNAseq
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
1
reply
1.1k
views
Edit: How to analyze matched pairs RNA sequencing data over multiple time points using DESeq2?
deseq2 rnaseq ribotag trap
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
4
votes
7
replies
2.3k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 5.8 years ago by 53k • written 5.8 years ago by ▴ 60
1
vote
3
replies
1.4k
views
Collapse Technical Replicates and Group-specific condition effects, individuals nested within groups
deseq2 RNAseq model.matrix collapseTechnicalReplicates
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 50
3
votes
2
replies
1.9k
views
tximeta error in fetching genome info
rnaseq tximeta
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
3
votes
6
replies
4.6k
views
Understanding voom behavior when model matrix is used with/without intercept for a continuous variable
limma voom rnaseq model.matrix intercept
updated 5.9 years ago by 53k • written 5.9 years ago by ▴ 30
0
votes
1
reply
1.9k
views
DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
0
votes
2
replies
1.2k
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq splicing RNAseq DEXSeq
written 5.9 years ago by ▴ 10
3
votes
1
reply
820
views
Can tximport be used to mitigate sample specific length biases?
RNASeq tximport
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 30
2
votes
3
replies
1.5k
views
How to correctly set up the design in DESeq2 for RRPP?
deseq2 rrpp DEGs RNAseq
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
2
votes
3
replies
2.4k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
1
vote
7
replies
3.7k
views
EdgeR RNAseq -- best way to deal with random effects
edger rnaseq
updated 5.9 years ago by • 0 • written 6.9 years ago by • 0
1
vote
3
replies
1.5k
views
How can I run a paired RankProd analysis in R?
RankProd paired RNAseq R
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
4
votes
5
replies
1.3k
views
Defining the design for a complicated multi-level experiment in Limma
limma RNASeq R voom
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 60
2
votes
2
replies
3.7k
views
DESeq2: design = ~1 For Normalisation Only.
deseq2 limma normalization tcga rnaseq
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
0
replies
823
views
Pathviews for DE list of genes
pathviews RNAseq Pathway analysis
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
2
votes
4
replies
1.1k
views
Combining RSEM Files with dif row # for tximport
tximport DEseq2 RNAseq
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
5
votes
8
replies
2.6k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 6.0 years ago by ★ 13k • written 6.0 years ago by ▴ 30
3
votes
4
replies
1.8k
views
How to normalize RNA-seq data if majority of transcripts expected to be differentially expressed vs control condition?
rnaseq edger
updated 6.0 years ago by 53k • written 6.0 years ago by • 0
0
votes
0
replies
1.1k
views
pvaluecutoff meaning in enrichKEGG
KEGG RNAseq
6.0 years ago sportiellomike • 0
3
votes
2
replies
2.7k
views
Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 10
4
votes
3
replies
5.1k
views
Differential gene expression anlaysis?
rnaseq R normalization
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 30
1
vote
1
reply
1.4k
views
cpm filtering parameter
cpm filtering transcriptomics rnaseq edgeR metatranscriptomics
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 10
1
vote
1
reply
1.0k
views
DESeq2 RNAseq differential expression analysis
deseq2 rnaseq
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
votes
4
replies
1.8k
views
DESeq2 unpaired RNAseq analysis
deseq2 rnaseq
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
1
vote
5
replies
1.8k
views
DESeq2: Normalization of allele specific counts in RNA-seq
deseq2 rnaseq allele-specific normalization
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 20
0
votes
6
replies
3.3k
views
Removing Batch effect on the raw counts or normalised counts
DEseq2 batch effect RNAseq
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 30
7
votes
4
replies
3.1k
views
RNA-seq normalization without filtering
deseq2 edger normalization RNAseq
updated 6.2 years ago by ★ 13k • written 6.2 years ago by ▴ 50
0
votes
10
replies
3.2k
views
tximport Error in attr(x, "names") <- as.character(value) : 'names' attribute [2] must be the same length as the vector [1]
software error RNAseq tximport R
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
2
replies
5.3k
views
Heatmap of selected genes
heatmap DEGs RNAseq DESeq2
updated 6.2 years ago by ▴ 280 • written 6.2 years ago by • 0
0
votes
2
replies
1.4k
views
Contrast vs relevel (DESEq2)
deseq2 RNAseq
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
4
votes
3
replies
25k
views
Fisher test in Rna seq
rna-seq rnaseq r
updated 6.2 years ago by 53k • written 6.8 years ago by • 0
0
votes
1
reply
1.0k
views
RNASeq biplot variables and samples
deseq2 rnaseq
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 30
0
votes
6
replies
2.3k
views
deseq2 pre filter rna seq
deseq2 rnaseq
updated 2.0 years ago by 43k • written 6.3 years ago by • 0
10
votes
8
replies
4.6k
views
Best alternative annotation package to BiomaRt
R biomaRt Ensembl rnaseq
6.3 years ago m93 ▴ 10
0
votes
4
replies
2.4k
views
DESeq2 compare all_vs_all levels error
deseq2 error RNAseq
updated 6.3 years ago by ★ 1.4k • written 6.3 years ago by ▴ 30
0
votes
1
reply
2.0k
views
Downloading HTSeq raw reads with TCGABiolinks
TCGAbiolinks RNASEQ
6.3 years ago sherajilir • 0
8
votes
7
replies
2.6k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
updated 6.3 years ago by • 0 • written 7.1 years ago by ▴ 20
3
votes
7
replies
4.5k
views
How to determine the cause of no difference between treatments in rnaseq?
RNAseq DGE edger
updated 6.3 years ago by 53k • written 6.3 years ago by • 0
0
votes
0
replies
1.2k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
6.3 years ago garbuzov • 0
0
votes
6
replies
2.2k
views
Plot genes with similar expression patterns
deseq2 R RNASeq
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 30
2
votes
4
replies
6.0k
views
edgeR and batch effect correction for differential analysis
edger limma r rnaseq batcheffect
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
0
votes
2
replies
1.3k
views
How to create design matrix for differential analysis within the same cell-line samples?
edger r differentialanalysis rnaseq designmatrix
updated 6.4 years ago by ★ 29k • written 6.4 years ago by ▴ 60
4
votes
3
replies
1.4k
views
WGCNA from different lengths RNAseq read
wgcna network co-expression rnaseq
updated 6.4 years ago by ★ 3.0k • written 6.4 years ago by ▴ 80
1,409 results • Page 10 of 29
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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