Showing : rnaseq • reset
3
votes
5
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244
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
1 day ago MedocRafael • 0
4
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2
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706
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
8 days ago • updated 1 day ago mila ▴ 10
0
votes
3
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268
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 3 days ago by ★ 4.2k • written 3 days ago by • 0
1
vote
4
replies
917
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
17 days ago • updated 4 days ago Lucy ▴ 60
0
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3
replies
241
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
updated 16 days ago by 51k • written 16 days ago by • 0
0
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0
replies
149
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
29 days ago JG13 • 0
0
votes
1
reply
211
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 5 weeks ago by 66k • written 5 weeks ago by • 0
1
vote
9
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606
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 5 weeks ago by 66k • written 6 weeks ago by • 0
1
vote
3
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332
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 6 weeks ago by 66k • written 6 weeks ago by ▴ 50
2
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2
replies
449
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 7 weeks ago by • 0 • written 9 weeks ago by • 0
0
votes
6
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783
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
9 weeks ago • updated 8 weeks ago atan • 0
2
votes
2
replies
289
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
9 weeks ago mohammedtoufiq91 ▴ 10
0
votes
0
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139
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
9 weeks ago Bibi • 0
10
votes
11
replies
2.1k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 9 weeks ago by • 0 • written 6.9 years ago by ▴ 80
1
vote
3
replies
402
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 10 weeks ago by 51k • written 10 weeks ago by • 0
0
votes
3
replies
414
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 12 weeks ago by ★ 4.2k • written 12 weeks ago by • 0
0
votes
1
reply
270
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 3 months ago by 42k • written 3 months ago by • 0
0
votes
2
replies
288
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 3 months ago by • 0
0
votes
2
replies
366
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
3 months ago catv • 0
5
votes
3
replies
492
views
Log-cpm values from limma
limma edgeR RNASeq
updated 11 weeks ago by 51k • written 3 months ago by • 0
0
votes
1
reply
258
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 3 months ago by 42k • written 3 months ago by • 0
0
votes
1
reply
236
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 3 months ago by ★ 4.2k • written 3 months ago by • 0
0
votes
2
replies
485
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
4 months ago kcarey • 0
2
votes
2
replies
369
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
4 months ago Sabiha ▴ 20
0
votes
2
replies
536
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
4 months ago kcarey • 0
1
vote
4
replies
421
views
DESeq2 Replicates
DESeq2 RNASeq
4 months ago kcarey • 0
1
vote
3
replies
488
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 4 months ago by ★ 1.4k • written 4 months ago by ▴ 10
0
votes
4
replies
460
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
5 months ago • updated 4 months ago mperalc • 0
0
votes
2
replies
510
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 5 months ago by 51k • written 5 months ago by • 0
3
votes
5
replies
802
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 4 months ago by 42k • written 5 months ago by ▴ 10
2
votes
1
reply
356
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 5 months ago by 42k • written 5 months ago by ▴ 10
3
votes
6
replies
825
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
5 months ago boczniak767 ▴ 740
0
votes
0
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361
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
5 months ago Abril • 0
2
votes
2
replies
636
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
5 months ago jackafiore • 0
1
vote
2
replies
1.4k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 14 months ago by • 0
0
votes
4
replies
545
views
Ballgown error in scan for c.tab files
ballgown RNASeq
5 months ago candacenewcome • 0
1
vote
3
replies
479
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
5 months ago island • 0
1
vote
3
replies
747
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 6 months ago by • 0
0
votes
1
reply
339
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 6 months ago by ▴ 210 • written 6 months ago by • 0
2
votes
4
replies
962
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
6 months ago Sabiha ▴ 20
4
votes
6
replies
797
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 5 months ago by 51k • written 6 months ago by • 0
3
votes
1
reply
429
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 6 months ago by 51k • written 6 months ago by • 0
0
votes
3
replies
745
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 6 months ago by • 0
0
votes
1
reply
369
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
6 months ago WS • 0
2
votes
3
replies
1.7k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 7 months ago by ★ 1.4k • written 7 months ago by • 0
1
vote
2
replies
593
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
7 months ago Sabiha ▴ 20
1
vote
2
replies
585
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
7 months ago drewhaydensteele • 0
7
votes
2
replies
1.1k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 7 months ago by 51k • written 7 months ago by • 0
0
votes
3
replies
604
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
8 months ago • updated 7 months ago Karthik • 0
1
vote
1
reply
454
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 8 months ago by 42k • written 8 months ago by • 0
50 results • Page 1 of 1
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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