Showing : RNASEQ • reset
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
updated 6 hours ago by 67k • written 1 day ago by • 0
0
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0
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38
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
1 day ago brayas13 • 0
3
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11
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625
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 29 days ago by • 0
2
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4
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339
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
28 days ago jihoon.kim.1495 ▴ 10
1
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1
reply
210
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
1
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2
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404
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 weeks ago by 42k • written 6 weeks ago by ▴ 10
0
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3
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343
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
5 weeks ago Travis • 0
0
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5
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1.6k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.5 years ago by • 0
0
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2
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823
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 9 weeks ago by ★ 1.4k • written 9 weeks ago by • 0
3
votes
5
replies
842
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 12 weeks ago by ★ 1.4k • written 3 months ago by • 0
2
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3
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454
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
12 weeks ago BioinfGuru ▴ 70
3
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6
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765
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 3 months ago by • 0
4
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3
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1.2k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 3 months ago by ▴ 10
0
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3
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531
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 3 months ago by ★ 4.5k • written 3 months ago by • 0
1
vote
4
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1.3k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
3 months ago Lucy ▴ 60
0
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4
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529
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 3 months ago by • 0
0
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0
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283
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
4 months ago JG13 • 0
0
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1
reply
333
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 4 months ago by 67k • written 4 months ago by • 0
1
vote
9
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1.2k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 4 months ago by 67k • written 4 months ago by ▴ 10
1
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3
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520
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 4 months ago by 67k • written 4 months ago by ▴ 50
2
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2
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590
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 5 months ago by ▴ 10 • written 5 months ago by • 0
0
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6
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1.1k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
5 months ago atan • 0
3
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2
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588
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
5 months ago mohammedtoufiq91 ▴ 10
0
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0
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266
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
5 months ago Bibi • 0
10
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11
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2.3k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 5 months ago by • 0 • written 7.2 years ago by ▴ 80
1
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3
replies
586
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 5 months ago by 51k • written 5 months ago by • 0
0
votes
3
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674
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 months ago by ★ 4.5k • written 6 months ago by • 0
0
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1
reply
433
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 6 months ago by 42k • written 6 months ago by • 0
0
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2
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421
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 6 months ago by • 0
0
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2
replies
543
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
6 months ago catv • 0
5
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3
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778
views
Log-cpm values from limma
limma edgeR RNASeq
updated 5 months ago by 51k • written 6 months ago by • 0
0
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1
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517
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 6 months ago by 42k • written 6 months ago by • 0
0
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1
reply
454
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 6 months ago by ★ 4.5k • written 7 months ago by • 0
0
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2
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904
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
7 months ago kcarey • 0
2
votes
2
replies
485
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 months ago Sabiha ▴ 20
0
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2
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1.1k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
7 months ago kcarey • 0
1
vote
4
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515
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DESeq2 Replicates
DESeq2 RNASeq
8 months ago kcarey • 0
1
vote
3
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625
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 8 months ago by ★ 1.4k • written 8 months ago by ▴ 10
0
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4
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625
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
8 months ago mperalc • 0
0
votes
2
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704
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 8 months ago by 51k • written 8 months ago by • 0
3
votes
5
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1.0k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 months ago by 42k • written 8 months ago by ▴ 10
2
votes
1
reply
471
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 months ago by 42k • written 8 months ago by ▴ 10
3
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6
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1.1k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
8 months ago boczniak767 ▴ 740
0
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0
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473
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
8 months ago Abril • 0
2
votes
2
replies
932
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
9 months ago jackafiore • 0
1
vote
2
replies
1.7k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 18 months ago by • 0
0
votes
4
replies
672
views
Ballgown error in scan for c.tab files
ballgown RNASeq
9 months ago candacenewcome • 0
1
vote
3
replies
627
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
9 months ago island • 0
1
vote
3
replies
928
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 9 months ago by • 0
0
votes
1
reply
455
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 9 months ago by ▴ 210 • written 9 months ago by • 0
50 results • Page 1 of 1
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Comment: Consistent Decimals In Data After Antibody Array Background Correction Using Lim by Ai • 0
Hi Gordon, Thank you so much for answering my question and confirming that this is expected! I will go ahead note this down. Sincerely, …
Answer: Annotation for EPICv2 by icecreamlover • 0
Hello, I am also working on analyzing my data from EPICv2 using ChAMP. I used this resource as a guide: https://github.com/YuanTian1991/ChA…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by James W. MacDonald 67k
And it doesn't matter if you're doing gene set analyses after, if the statistics are questionable to begin with.
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by James W. MacDonald 67k
If you're saying that (as an example) you have treated and control in both assay types, and you want to combine and make comparisons betwee…
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k
I have contacted NCBI, and meanwhile got an an answer. See below. It turns out that the official, HGNC-approved symbols are present in the…
Votes
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
Answer: DecideTest vs topTAGs in edgeR
Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
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