Showing : RNAseq • reset
2
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2
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975
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 16 months ago by ▴ 10 • written 16 months ago by • 0
0
votes
6
replies
2.1k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
16 months ago atan • 0
3
votes
2
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1.2k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
16 months ago mohammedtoufiq91 ▴ 10
0
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0
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603
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
16 months ago Bibi • 0
10
votes
11
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3.0k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 16 months ago by • 0 • written 8.1 years ago by ▴ 80
1
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3
replies
1.0k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 17 months ago by 53k • written 17 months ago by • 0
0
votes
3
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1.4k
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
0
votes
1
reply
808
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 17 months ago by 43k • written 17 months ago by • 0
0
votes
2
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737
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 17 months ago by • 0
0
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2
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1.1k
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
17 months ago catv • 0
5
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3
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1.5k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 17 months ago by 53k • written 17 months ago by • 0
0
votes
1
reply
1.2k
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 17 months ago by 43k • written 17 months ago by • 0
0
votes
1
reply
915
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
0
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2
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1.9k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
18 months ago kcarey • 0
2
votes
2
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775
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
19 months ago Sabiha ▴ 20
0
votes
2
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3.0k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
19 months ago kcarey • 0
1
vote
4
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867
views
DESeq2 Replicates
DESeq2 RNASeq
19 months ago kcarey • 0
1
vote
3
replies
1.0k
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 19 months ago by ★ 1.4k • written 19 months ago by ▴ 10
0
votes
4
replies
975
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
19 months ago mperalc • 0
0
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2
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1.1k
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 19 months ago by 53k • written 19 months ago by • 0
3
votes
5
replies
1.6k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 19 months ago by 43k • written 19 months ago by ▴ 10
2
votes
1
reply
704
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 19 months ago by 43k • written 19 months ago by ▴ 10
3
votes
7
replies
1.8k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
19 months ago • updated 27 days ago boczniak767 ▴ 740
0
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0
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730
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
20 months ago Abril • 0
2
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2
replies
1.7k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
20 months ago jackafiore • 0
1
vote
2
replies
2.4k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.4 years ago by • 0
0
votes
4
replies
970
views
Ballgown error in scan for c.tab files
ballgown RNASeq
20 months ago candacenewcome • 0
1
vote
3
replies
1.1k
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
20 months ago island • 0
1
vote
3
replies
1.3k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 20 months ago by • 0
0
votes
1
reply
623
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 20 months ago by ▴ 220 • written 20 months ago by • 0
2
votes
4
replies
2.1k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
20 months ago Sabiha ▴ 20
4
votes
6
replies
1.6k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 20 months ago by 53k • written 21 months ago by • 0
3
votes
1
reply
822
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 21 months ago by 53k • written 21 months ago by • 0
0
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3
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1.5k
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 21 months ago by • 0
0
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1
reply
740
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
21 months ago WS • 0
2
votes
3
replies
3.5k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 21 months ago by ★ 1.4k • written 22 months ago by • 0
1
vote
2
replies
1.2k
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
21 months ago Sabiha ▴ 20
1
vote
2
replies
1.1k
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
22 months ago drewhaydensteele • 0
12
votes
5
replies
4.9k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by • 0 • written 22 months ago by • 0
0
votes
3
replies
1.2k
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
22 months ago Karthik • 0
1
vote
1
reply
726
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
2
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3
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1.4k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
22 months ago Karthik • 0
2
votes
2
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1.0k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
22 months ago Manthos • 0
2
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4
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1.4k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
23 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
773
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
0
votes
2
replies
1.3k
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 23 months ago by ★ 1.1k • written 23 months ago by ▴ 200
0
votes
9
replies
3.1k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 23 months ago by • 0 • written 7.9 years ago by ▴ 60
1
vote
4
replies
1.4k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
23 months ago Wending • 0
0
votes
0
replies
803
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
23 months ago mch • 0
5
votes
2
replies
2.1k
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 23 months ago by 53k • written 23 months ago by ▴ 10
1,409 results • Page 2 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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