Showing : RNAseq • reset
2
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2
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2.0k
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Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS PCA RNASeq MDS
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 60
0
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4
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1.2k
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limma: Genes Associated with Continuous Predictor in Subsets of Samples
RNASeq limma
3.6 years ago • updated 3.5 years ago danphillips28 ▴ 10
0
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1
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2.2k
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GSEA using custom GO annotations
RNASeq GSEA
updated 3.6 years ago by ★ 3.4k • written 3.6 years ago by ▴ 10
0
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1
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2.8k
views
Edge R Error in quantile.default(zresid, probs = prob) : missing values and NaN's not allowed if 'na.rm' is FALSE
diffSpliceDGE RNASeq DifferentialSplicingWorkflow AlternativeSplicing edgeR
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
4
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1
reply
3.6k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 40
1
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1
reply
973
views
Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 40
4
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6
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13k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
3.6 years ago treebig44 ▴ 40
0
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0
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1.2k
views
Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
2
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2
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1.7k
views
Complex contrasts in limma
RNASeq limma DifferentialExpression
3.6 years ago tcalvo ▴ 100
0
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2
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920
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Differential expression in fixed windows
DESeq2 RNASeq
3.6 years ago anatmela • 0
2
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1
reply
1.2k
views
DESeq2 handling of replicates
DESeq2 RNASeq limma
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
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1
reply
1.3k
views
Controlling for sex variance in Galaxy DESeq2
DESeq2 RNASeq Galaxy
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
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1
reply
2.3k
views
95% Confidence intervals for Fold Changes computed by DESeq2
DESeq2 RNASeq
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
0
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1
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1.9k
views
Exporting org.*.*.db Gene Ontology annotations to excel sheet or txt
OrgDb RNASeq
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
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4
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2.2k
views
How do you get averages of each group in Limma output
RNASeq limma
3.7 years ago Matthew • 0
0
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6
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5.3k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 60
0
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4
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1.8k
views
Multi-factor paired RNAseq differential analysis with DEseq2
DESeq2 RNASeq
updated 3.7 years ago by ★ 1.4k • written 3.7 years ago by • 0
0
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3
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3.4k
views
DESeq2 contrast multiple treated conditions versus multiple control conditions
RNASeq DESeq2
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
0
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3
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2.7k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 90
1
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3
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2.0k
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 2.7 years ago by • 0 • written 3.7 years ago by • 0
0
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2
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1.3k
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Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
3.7 years ago IamFrofro • 0
0
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0
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820
views
RNA seq of 4 groups p_values
R analysis p_values RNASeq
updated 3.7 years ago by 21k • written 3.7 years ago by • 0
0
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0
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1.5k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
3
votes
5
replies
4.6k
views
DESeq2 median of ratios normalization for signature score calculation
MRN RNASeq Normalization DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 10
1
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3
replies
2.3k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
votes
1
reply
1.4k
views
RNAseq using galaxy
RNASeq
updated 3.8 years ago by ★ 5.0k • written 3.8 years ago by • 0
0
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0
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809
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Complex design in DESeq2 doesn't seem to be supported in Glimma
limma Glimma RNASeq DESeq2
3.8 years ago Jonas • 0
0
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0
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1.4k
views
Glimma: Error: Length of groups must be equal to the number of columns in counts
Glimma RNASeq
3.8 years ago Jonas • 0
0
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2
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1.4k
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 3.8 years ago by ★ 13k • written 3.8 years ago by • 0
0
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0
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1.5k
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gene id mapping issue
RNASeq
3.8 years ago waltsonwang88 • 0
0
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1
reply
1.5k
views
Outlier Removal WGCNA
RNASeq WGCNA
updated 3.8 years ago by 6.7k • written 3.8 years ago by ▴ 10
2
votes
9
replies
6.1k
views
Deseq2 normalization for WGCNA
RNASeq Deseq2 DESeq2 WGCNA
updated 3.4 years ago by 43k • written 3.8 years ago by ▴ 10
4
votes
4
replies
3.4k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 22 months ago by 53k • written 3.8 years ago by ▴ 10
0
votes
1
reply
957
views
RNA-Seq Workflow Vignette - library(airway) Missing "quants" directory
RNASeq DESeq2 airway
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
3
votes
5
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3.6k
views
limma-trend and voom results do not agree
limma limma-trend voom RNASeq
3.9 years ago • updated 3.8 years ago Tyler Sagendorf ▴ 10
1
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1
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1.1k
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
1
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2
replies
3.6k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 10
0
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1
reply
1.4k
views
Trouble with gene dendrogram
Network RNASeq WGCNA
updated 2.7 years ago by • 0 • written 3.9 years ago by ▴ 10
0
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3
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2.3k
views
Problem getting soft threshold power using WGCNA for RNA-seq data
RNASeq WGCNA
3.9 years ago jms2520 ▴ 10
4
votes
1
reply
1.9k
views
Elastic Net for RNAseq data
Bioconductor RNASeq
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 20
2
votes
3
replies
2.6k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 3.9 years ago by 68k • written 3.9 years ago by ▴ 20
0
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1
reply
1.5k
views
Calculating gene expression dominance coefficient via DESeq2
RNASeq DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
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1
reply
1.6k
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Summarising WGCNA data with modules and their corresponding gene ID and statistics
RNASeq WGCNA
3.9 years ago synat.keam • 0
1
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2
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1.5k
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Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
3.9 years ago Barista • 0
0
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0
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787
views
Gene expression changes in one condition
RNASeq Gene ExpressionData
3.9 years ago AZ ▴ 30
0
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0
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1.0k
views
Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
3.9 years ago svlachavas ▴ 840
4
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4
replies
6.6k
views
FeatureCounts
counts subread RNASeq featurecounts
3.9 years ago k___ ▴ 30
1
vote
3
replies
2.6k
views
Rsamtools : Extracting Unmapped Reads from BAM file
Unmapped RNAseq Rsamtools
3.9 years ago polemiraza ▴ 70
3
votes
3
replies
990
views
Is comparison of data without pairwise comparison in batches possible? Or even reasonable?
RNASeq DESeq2
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 20
4
votes
1
reply
3.1k
views
mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 10
1,409 results • Page 6 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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