Showing : differentialexpression • reset
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 24 months ago by 43k • written 24 months ago by ▴ 20
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2
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888
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 24 months ago by 43k • written 24 months ago by • 0
5
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6
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1.7k
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
2.0 years ago Shaimaa Gamal • 0
4
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6
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1.8k
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 24 months ago by 53k • written 2.0 years ago by • 0
3
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1
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958
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
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3
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1.3k
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 2.1 years ago by • 0
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5
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1.5k
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Help with model for differential expression analysis
DifferentialExpression edgeR
2.1 years ago • updated 2.0 years ago Lucy ▴ 60
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3
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1.2k
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
1
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1
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1.0k
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
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4
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1.3k
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
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2
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1.6k
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
2.1 years ago Luca • 0
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2
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1.5k
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
0
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1
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823
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 10
1
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4
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1.3k
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 60
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8
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1.7k
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Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
2.2 years ago Luca • 0
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0
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961
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clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
2.3 years ago nromerov • 0
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6
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1.7k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 2.3 years ago by 16k • written 2.3 years ago by • 0
2
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4
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1.7k
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
2.3 years ago Shihui • 0
0
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1
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867
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''Model_Matrix'' error
DifferentialExpression limma
updated 2.3 years ago by 53k • written 2.4 years ago by • 0
3
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3
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1.1k
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comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
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3
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946
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how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
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2
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1.1k
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
2.4 years ago Beyza • 0
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1
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877
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Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
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1
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879
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Is it possible to use pre-ranked list in EGSEA?
EGSEA EGSEAdata EGSEA123 DifferentialExpression
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
2
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7
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5.6k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 2.4 years ago by • 0 • written 4.8 years ago by ▴ 20
1
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3
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1.3k
views
DESeq differential expression results are too stringet. How to relax my criteria
shrinkage DifferentialExpression DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by ▴ 10
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0
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845
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DEG after deconvolution of GeoMx Spatial data using scRNA-seq reference
GeoMx DifferentialExpression GeomxTools
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
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6
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1.5k
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
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2
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1.4k
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Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
2.5 years ago Matteo • 0
1
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1
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1.0k
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NA p values in edgeR results
DifferentialExpression edgeR
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
2
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8
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3.4k
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Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 2.6 years ago by ▴ 10
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3
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1.1k
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limma paired design
DifferentialExpression limma
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
0
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1
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890
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Design formula for genotype-specific condition effects using ~group in the design
RNASeqData DifferentialExpression DESeq2
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
1
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0
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1.1k
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 20
2
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6
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2.0k
views
How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 2.6 years ago by 4.3k • written 2.7 years ago by • 0
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4
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1.4k
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
2.7 years ago sreeshmaraj72 • 0
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1
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1.0k
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DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
3
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3
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2.0k
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Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by ▴ 20
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1.2k
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LIMMA: design with paired samples within and across treatments
DifferentialExpression limma
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
0
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4
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2.4k
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enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
2.7 years ago ruba-mahmoud • 0
1
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2
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1.2k
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
0
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2
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1.3k
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DESeq: low p-values for genes with zero counts in all but one sample of the compared groups
DESeq2 DifferentialExpression
2.7 years ago António Miguel de Jesus Domingues ▴ 510
1
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2
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871
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Contrast of Contrasts in Limma
limma DifferentialExpression
2.7 years ago mpitz • 0
1
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3
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1.7k
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
2
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2
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1.9k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 20
1
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2
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1.6k
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Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.8 years ago AZ ▴ 20
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0
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785
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Limma: Models containing an intercept and interactions with continuous variables.
limma edgeR DifferentialExpression
2.9 years ago Aashil • 0
0
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1
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1.5k
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Analyse of MASS spectrometry proteomics data
DifferentialExpression MassSpectrometry
updated 2.9 years ago by • 0 • written 3.4 years ago by • 0
3
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6
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2.5k
views
do I have to do this step in creating DGEList ?
DifferentialExpression
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
0
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3
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1.5k
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Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
202 results • Page 2 of 5
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Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Comment: limpa analysis advice by Gordon Smyth 53k
I prefer for limpa to work on precursor intensities, because my understanding is that precursors are the basic unit of identification and q…
Answer: Confirm that OpenStats will not be archived (pryr dependency) by shepherl 4.3k
As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Michael Love 43k
Yes, I find that the LFC shrinkage and its corresponding stat `svalue` if you use lfcShrink with a threshold often returns more reliable ge…
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Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
Answer: Array weights in dpcDE
Answer: Array weights in dpcDE
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