Showing : RNAseq • reset
1
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6
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6.4k
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How to perform multiple pairwise comparisons
deseq2 bioconductor rnaseq
updated 2.8 years ago by 43k • written 9.0 years ago by ▴ 10
0
votes
5
replies
11k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 19 months ago by • 0 • written 9.0 years ago by • 0
1
vote
3
replies
1.8k
views
Interaction term analysis using ballgown
ballgown stringtie voom limma differential gene expression rnaseq
updated 9.0 years ago by ▴ 210 • written 9.0 years ago by ▴ 10
0
votes
3
replies
3.6k
views
Fisher exact test
rnaseq differential gene expression
updated 9.0 years ago by ▴ 980 • written 9.1 years ago by • 0
2
votes
23
replies
5.1k
views
Coping with a label/class imbalance in DESeq2
deseq2 rnaseq r regression
updated 9.0 years ago by 43k • written 9.1 years ago by • 0
0
votes
1
reply
1.7k
views
FeatureCounts Assertion `l_name < 100' failed.
featurecounts rnaseq
9.1 years ago shg018 • 0
0
votes
1
reply
1.2k
views
Gviz error after updating R
software error Gviz chipseq rnaseq
9.1 years ago ta_awwad ▴ 10
6
votes
3
replies
1.4k
views
How to deal with these data with DESeq2 ?? In hurry!
deseq2 normalization rnaseq
updated 9.1 years ago by 43k • written 9.1 years ago by • 0
0
votes
13
replies
5.0k
views
DESeq2: collapseReplicates error
deseq2 rnaseq differential gene expression
9.1 years ago ta_awwad ▴ 10
1
vote
13
replies
16k
views
Count matrix from Kallisto as input for DESeq2
rnaseq deseq2 kallisto
9.1 years ago yjliu1127 • 0
0
votes
5
replies
2.1k
views
Can Normalized cpm values be used as RUVs input
rnaseq ruvseq
updated 9.1 years ago by ▴ 980 • written 9.1 years ago by • 0
0
votes
5
replies
4.2k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 9.1 years ago by ▴ 280 • written 9.1 years ago by • 0
8
votes
8
replies
4.9k
views
Disagreement between TMM (edgeR) and RLE (DESeq) normalisation for single-cell data
rnaseq single cell normalization edgeR deseq2
updated 9.1 years ago by ★ 29k • written 9.1 years ago by ▴ 50
4
votes
4
replies
3.2k
views
design and contrast matrix for RNA seq analysis with three different controls
bioconductor edgeR design and contrast matrix rnaseq differential gene expression
updated 9.1 years ago by ★ 29k • written 9.1 years ago by • 0
0
votes
0
replies
1.4k
views
Error in SAMseq analysis with R
r samseq microarray rnaseq geneexpression
9.1 years ago namilio • 0
0
votes
10
replies
5.8k
views
Differential expression analysis for STAR-aligned RNA-Seq data
deseq2 rnaseq STAR
updated 9.1 years ago by 43k • written 9.1 years ago by • 0
1
vote
0
replies
2.0k
views
Pre-processing of RNA sequencing data for GSVA
rnaseq rna-seq preprocessing gsva
9.2 years ago t.kuilman ▴ 170
3
votes
6
replies
2.5k
views
Clarification MAplot and FDR in EdgeR
edgeR MAplot rnaseq differential gene expression
updated 9.2 years ago by 53k • written 9.2 years ago by • 0
1
vote
7
replies
3.7k
views
RNA-seq: two factor anova - how to find the variability explained by each of the factor?
rnaseq two factor anova limma DEseq2 edgeR
9.2 years ago nooshin ▴ 300
1
vote
2
replies
1.9k
views
Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R gage package rnaseq pathview
9.2 years ago joanito.liberti • 0
4
votes
2
replies
3.7k
views
WGCNA blockwiseModules parallelisation question
wgcna rnaseq
updated 9.2 years ago by ★ 3.0k • written 9.2 years ago by ▴ 10
0
votes
2
replies
1.6k
views
topgo rnaseq error
topgo rnaseq
9.2 years ago tarek.mohamed ▴ 10
0
votes
2
replies
2.9k
views
topGO fro RNA-seq
topgo rnaseq
9.2 years ago tarek.mohamed ▴ 10
3
votes
6
replies
2.0k
views
Mutation effect on expression (RNA-Seq) using limma
limma rnaseq mutations
updated 9.2 years ago by ★ 29k • written 9.2 years ago by ▴ 20
3
votes
5
replies
4.9k
views
DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 9.2 years ago by 43k • written 9.2 years ago by ▴ 10
2
votes
2
replies
1.3k
views
Ballgown Custom Model Question
ballgown rnaseq
updated 9.2 years ago by ▴ 650 • written 9.2 years ago by • 0
5
votes
4
replies
2.6k
views
Why does the filtering of lowly expressed genes for analysis with edgeR must be done unsupervised?
edgeR RNAseq DE analysis gene filtering
9.2 years ago Mau ▴ 50
1
vote
2
replies
1.4k
views
DEseq2 analysis for 2 batches of samples that are sequenced separately
deseq2 featurecounts rnaseq
updated 9.2 years ago by 68k • written 9.2 years ago by ▴ 20
3
votes
4
replies
2.1k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread rnaseq alignment
updated 9.2 years ago by 53k • written 9.2 years ago by • 0
8
votes
3
replies
1.9k
views
Counting ambiguously mapped reads per feature
rnaseq bam genomicranges GenomicAlignments Rsamtools
updated 9.2 years ago by 53k • written 9.2 years ago by ▴ 110
1
vote
1
reply
2.3k
views
Using pathview with uncommon species leads to Errors
pathview Kegg rnaseq data visualization
updated 9.2 years ago by ★ 1.6k • written 9.2 years ago by • 0
11
votes
9
replies
5.8k
views
How to remove more than two batches in my data-sets
limma RNAseq removebatcheffect()
updated 9.2 years ago by 53k • written 9.2 years ago by ▴ 30
1
vote
4
replies
1.7k
views
Polyester and mutations
rnaseq pair-end reads mutations
updated 9.2 years ago by ▴ 650 • written 9.2 years ago by • 0
0
votes
0
replies
1.2k
views
CummeRbund Expression Bar Plot
cummerbund rnaseq
9.2 years ago k1064622 • 0
4
votes
16
replies
9.1k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 19 months ago by • 0 • written 10.4 years ago by ▴ 160
3
votes
1
reply
6.5k
views
edgeR: exactTest, glmFIt or glmQLFit approach?
edger rnaseq glm glmfit
updated 9.3 years ago by ★ 29k • written 9.3 years ago by • 0
11
votes
7
replies
8.1k
views
What's the rationale for using the negative binomial distribution to model read counts?
rnaseq
updated 9.3 years ago by ★ 7.9k • written 9.3 years ago by ▴ 70
1
vote
1
reply
1.4k
views
Generating ExpressionSet Objects
r expressionset subseq rnaseq
updated 9.3 years ago by 25k • written 9.3 years ago by ▴ 70
0
votes
1
reply
1.5k
views
why my resultsNames(deseq) is not the same as model.matrix ?
deseq2 RNASeq SVA
updated 9.3 years ago by 43k • written 9.3 years ago by • 0
2
votes
1
reply
1.9k
views
polyester: adding noise to RNASeq counts?
rnaseq polyester
updated 9.3 years ago by ▴ 210 • written 9.3 years ago by • 0
9
votes
11
replies
11k
views
Filtering of RNA-seq data in EdgeR
rnaseq edger filtering
updated 9.3 years ago by ▴ 20 • written 9.4 years ago by ▴ 20
3
votes
4
replies
9.9k
views
DESeqDataSetFromMatrix giving error: "argument must be coercible to non-negative integer"
DESeqDataSet DESeqDataSetFromMatrix rnaseq deseq2
9.3 years ago ErickF ▴ 40
4
votes
3
replies
3.3k
views
Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
summarizeoverlaps rnaseq bplapply rangedsummarizedexperiment read counting
9.3 years ago ErickF ▴ 40
0
votes
2
replies
1.4k
views
Runing into error while trying GRanges from R
rnaseq bumphunter genomicranges
9.3 years ago alva.james • 0
15
votes
4
replies
3.7k
views
Using multiple tools for differential gene expression analysis as validation
edger limma deseq2 rnaseq
updated 9.3 years ago by ★ 7.9k • written 9.3 years ago by ▴ 130
14
votes
5
replies
9.0k
views
EDGE-R exact test vs QL F-test
edger rnaseq
updated 3.5 years ago by • 0 • written 9.3 years ago by ▴ 40
1
vote
4
replies
2.3k
views
Effect of treatment vs control over time in RNA Seq (edgeR and limma)
edgeR limma voom RNASeq multiple time points
updated 9.3 years ago by ★ 7.9k • written 9.3 years ago by ▴ 20
2
votes
1
reply
1.6k
views
Affy loess normalization of RNA-seq data
affy RNAseq loess
updated 9.3 years ago by ★ 29k • written 9.3 years ago by • 0
0
votes
3
replies
997
views
DESeq2 analysis returns 41% low count genes
deseq2 rnaseq
updated 9.3 years ago by 43k • written 9.3 years ago by ▴ 10
0
votes
4
replies
6.2k
views
10 multiple comparisons in DESeq2
deseq2 rnaseq statistics
updated 9.3 years ago by 43k • written 9.3 years ago by • 0
1,409 results • Page 20 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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