Showing : RNASeqData • reset
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My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
4 days ago cftattersfield • 0
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4
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215
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
10 days ago georgeyu703 • 0
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1
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133
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Correlation between gene clusters
genomes RNASeqData
written 26 days ago by • 0
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2
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265
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
28 days ago • updated 26 days ago gingergeiger22 • 0
2
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1
reply
358
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 29 days ago by 43k • written 5 weeks ago by • 0
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1
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196
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combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 5 weeks ago by • 0 • written 5 weeks ago by • 0
2
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1
reply
314
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
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4
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682
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
3 months ago Philippine • 0
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2
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390
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 3 months ago by • 0
3
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11
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863
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 3 months ago by • 0
1
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1
reply
444
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WGCNA
DEGselection RNASeqData WGCNA
updated 3 months ago by ▴ 760 • written 3 months ago by • 0
1
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1
reply
288
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 4 months ago by ★ 4.6k • written 4 months ago by • 0
1
vote
1
reply
508
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Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 4 months ago by 52k • written 5 months ago by • 0
1
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2
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1.5k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 5 months ago by • 0
1
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2
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375
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Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
5 months ago Gordon • 0
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3
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629
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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 6 months ago by ★ 4.6k • written 6 months ago by • 0
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4
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657
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 6 months ago by • 0
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3
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1.1k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
7 months ago Tanvi • 0
1
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3
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640
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 7 months ago by 67k • written 7 months ago by ▴ 50
0
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1
reply
405
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How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 8 months ago by 67k • written 8 months ago by • 0
0
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1
reply
414
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ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 4 months ago by ▴ 20 • written 8 months ago by • 0
0
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1
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431
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 9 months ago by 52k • written 9 months ago by • 0
0
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1
reply
368
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Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 10 months ago by 67k • written 10 months ago by • 0
3
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5
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1.2k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 11 months ago by 43k • written 11 months ago by ▴ 10
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0
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552
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
11 months ago Abril • 0
1
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2
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1.9k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 21 months ago by • 0
1
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3
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752
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
12 months ago island • 0
0
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2
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551
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
12 months ago Diana • 0
0
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1
reply
816
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
5
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6
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1.1k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
12 months ago Shaimaa Gamal • 0
1
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1
reply
693
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
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2
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809
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
13 months ago Luca • 0
0
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1
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1.1k
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Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 14 months ago by 67k • written 14 months ago by • 0
1
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2
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826
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
14 months ago drewhaydensteele • 0
1
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1
reply
678
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Differential gene expression analysis
RNASeqData RNAseq123
updated 14 months ago by ★ 4.6k • written 14 months ago by • 0
1
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2
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1.3k
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
14 months ago • updated 13 months ago Levi • 0
0
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3
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1.8k
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
14 months ago Oenone • 0
3
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4
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1.0k
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Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
14 months ago pl23 • 0
0
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1
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576
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 14 months ago by 43k • written 14 months ago by ▴ 10
2
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2
replies
747
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DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
14 months ago Manthos • 0
0
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1
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683
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DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 14 months ago by ★ 13k • written 14 months ago by • 0
0
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2
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730
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Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
15 months ago Ben ▴ 10
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2
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1.9k
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MA plot for DESEq2 analysis
RNASeqData DESeq2
15 months ago RHEA • 0
2
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3
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1.9k
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Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
1
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1
reply
777
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 15 months ago by 67k • written 15 months ago by • 0
1
vote
7
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1.3k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 14 months ago by 52k • written 16 months ago by • 0
0
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1
reply
723
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 16 months ago by ▴ 780 • written 16 months ago by • 0
2
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4
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1.2k
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
16 months ago Shihui • 0
0
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4
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1.1k
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 16 months ago by 67k • written 16 months ago by ▴ 10
3
votes
3
replies
2.6k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
16 months ago Ethan Nguyen • 0
50 results • Page 1 of 1
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Comment: Unused arguments error without used arguments in GSVA? by 1sunmic2 • 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA by User3088 • 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
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Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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