Showing : RnaSeq • reset
1
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 1 day ago by 66k • written 3 days ago by • 0
1
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3
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177
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 4 days ago by 66k • written 4 days ago by ▴ 50
2
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2
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365
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 12 days ago by • 0 • written 26 days ago by • 0
0
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6
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628
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
23 days ago • updated 17 days ago atan • 0
2
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2
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215
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
25 days ago • updated 24 days ago mohammedtoufiq91 ▴ 10
0
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0
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92
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
27 days ago Bibi • 0
10
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11
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2.0k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 24 days ago by • 0 • written 6.8 years ago by ▴ 80
1
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3
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333
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 4 weeks ago by 51k • written 4 weeks ago by • 0
0
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3
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295
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
0
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1
reply
200
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
0
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2
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227
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 7 weeks ago by • 0
0
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2
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286
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
8 weeks ago • updated 7 weeks ago catv • 0
5
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3
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380
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Log-cpm values from limma
limma edgeR RNASeq
updated 5 weeks ago by 51k • written 8 weeks ago by • 0
0
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1
reply
169
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
0
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1
reply
182
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 9 weeks ago by ★ 4.2k • written 9 weeks ago by • 0
0
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2
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366
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
12 weeks ago kcarey • 0
2
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2
replies
323
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
3 months ago Sabiha ▴ 20
0
votes
2
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412
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
3 months ago kcarey • 0
1
vote
4
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366
views
DESeq2 Replicates
DESeq2 RNASeq
3 months ago kcarey • 0
1
vote
3
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435
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 3 months ago by ★ 1.4k • written 3 months ago by ▴ 10
0
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4
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374
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
3 months ago mperalc • 0
0
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2
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408
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Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 3 months ago by 51k • written 3 months ago by • 0
3
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5
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722
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 3 months ago by 42k • written 3 months ago by ▴ 10
2
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1
reply
313
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 3 months ago by 42k • written 3 months ago by ▴ 10
3
votes
6
replies
685
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
3 months ago boczniak767 ▴ 740
0
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0
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289
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
4 months ago Abril • 0
2
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2
replies
517
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
4 months ago jackafiore • 0
1
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2
replies
1.3k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 13 months ago by • 0
0
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4
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482
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Ballgown error in scan for c.tab files
ballgown RNASeq
4 months ago candacenewcome • 0
1
vote
3
replies
407
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
4 months ago island • 0
1
vote
3
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667
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 4 months ago by • 0
0
votes
1
reply
297
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 4 months ago by ▴ 210 • written 4 months ago by • 0
2
votes
4
replies
782
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
4
votes
6
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712
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 4 months ago by 51k • written 5 months ago by • 0
3
votes
1
reply
371
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 5 months ago by 51k • written 5 months ago by • 0
0
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3
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634
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 5 months ago by • 0
0
votes
1
reply
312
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
5 months ago WS • 0
2
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3
replies
1.4k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 5 months ago by ★ 1.4k • written 6 months ago by • 0
1
vote
2
replies
535
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago Sabiha ▴ 20
1
vote
2
replies
507
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
6 months ago drewhaydensteele • 0
7
votes
2
replies
989
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 6 months ago by 51k • written 6 months ago by • 0
0
votes
3
replies
534
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
6 months ago Karthik • 0
1
vote
1
reply
418
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 6 months ago by 42k • written 6 months ago by • 0
2
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3
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603
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DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
6 months ago Karthik • 0
2
votes
2
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474
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
6 months ago Manthos • 0
2
votes
4
replies
686
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
7 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
475
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
0
votes
2
replies
592
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 7 months ago by ★ 1.1k • written 7 months ago by ▴ 190
0
votes
9
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2.6k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 7 months ago by • 0 • written 6.6 years ago by ▴ 60
1
vote
4
replies
702
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
7 months ago Wending • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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