Showing : RNASeqData • reset
22
votes
15
replies
7.6k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 6 months ago by ▴ 10 • written 2.1 years ago by ▴ 50
8
votes
2
replies
7.0k
views
handling outliers with DESeq2
RNASeqData DESeq2 Outliers
3.1 years ago paty ▴ 60
7
votes
5
replies
3.5k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
3.5 years ago ecg1g15 ▴ 20
6
votes
4
replies
11k
views
How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 2.4 years ago by • 0 • written 3.2 years ago by ▴ 10
5
votes
6
replies
606
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
4 months ago • updated 3 months ago Shaimaa Gamal • 0
4
votes
1
reply
2.4k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 2.2 years ago by 42k • written 2.2 years ago by ▴ 30
4
votes
3
replies
1.2k
views
Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by ▴ 10
3
votes
6
replies
1.3k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 3.5 years ago by 42k • written 3.5 years ago by ▴ 50
3
votes
4
replies
1.4k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.1 years ago hgalmoore • 0
3
votes
5
replies
671
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 12 weeks ago by ▴ 10
3
votes
3
replies
986
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
10 months ago amnahsiddiqa ▴ 10
3
votes
2
replies
943
views
Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
3.2 years ago Wuschel ▴ 10
3
votes
3
replies
1.4k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
24 months ago • updated 23 months ago JK Kim ▴ 20
3
votes
6
replies
8.9k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
2.2 years ago treebig44 ▴ 30
3
votes
4
replies
560
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
3
votes
2
replies
689
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 11 months ago by 50k • written 11 months ago by ▴ 10
3
votes
3
replies
1.3k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
8 months ago Ethan Nguyen • 0
3
votes
2
replies
969
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.1 years ago • updated 2.0 years ago Dakarai ▴ 10
2
votes
1
reply
720
views
Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData DataImport oligo RNASeqData convert
updated 10 months ago by 65k • written 10 months ago by • 0
2
votes
9
replies
2.3k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
23 months ago Peipei • 0
2
votes
2
replies
440
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
727
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
2
votes
3
replies
1.1k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 9 months ago by 65k • written 9 months ago by ▴ 10
2
votes
3
replies
1.2k
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
2.0 years ago Maka • 0
2
votes
4
replies
2.8k
views
Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
3.5 years ago ecg1g15 ▴ 20
2
votes
3
replies
1.4k
views
RNA-seq analysis without replicates
DESeq2 RESEQ RNASeqData
updated 13 months ago by • 0 • written 13 months ago by • 0
2
votes
8
replies
2.4k
views
While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
2
votes
4
replies
1.2k
views
DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
2.7 years ago khaveh ▴ 10
2
votes
3
replies
1.2k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 4 weeks ago by • 0 • written 11 months ago by • 0
2
votes
3
replies
857
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
1
vote
1
reply
420
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
1
vote
1
reply
471
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 10 months ago by 50k • written 10 months ago by • 0
1
vote
1
reply
662
views
Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 2.2 years ago by 42k • written 2.2 years ago by ▴ 30
1
vote
7
replies
881
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 7 months ago by • 0
1
vote
1
reply
794
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 2.2 years ago by 50k • written 2.2 years ago by • 0
1
vote
1
reply
354
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
1
vote
6
replies
1.4k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
3.3 years ago Seaweed • 0
1
vote
1
reply
773
views
NOIseq Probability column
RNAseq RNASeqData NOISeq
23 months ago Pratibha ▴ 10
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
1
vote
2
replies
700
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
5 months ago • updated 4 months ago Levi • 0
1
vote
2
replies
2.7k
views
Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 20 months ago by ★ 1.4k • written 20 months ago by • 0
1
vote
5
replies
1.2k
views
Error in DEseq
DEseq RNASeqData
updated 23 months ago by ★ 4.1k • written 23 months ago by • 0
1
vote
2
replies
838
views
Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
2.2 years ago • updated 2.1 years ago m.glymenaki • 0
1
vote
1
reply
1.2k
views
Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 2.6 years ago by 50k • written 2.6 years ago by • 0
1
vote
1
reply
2.2k
views
Limma interaction term
RNASeqData limma DifferentialExpression
updated 2.2 years ago by 50k • written 2.2 years ago by • 0
1
vote
2
replies
693
views
Installation of R-packages for RNA-seq analysis
RNASeqData
15 months ago Begin-R • 0
1
vote
4
replies
1.3k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2 Log2FC RNASeqData
16 months ago Iwan • 0
1
vote
9
replies
912
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by jane • 0
Your material was totally correct, therefore I was able to learn what I needed to know. I'd want to convey my heartfelt gratitude for shari…
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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