Showing : RNASeqData • reset
22
votes
15
replies
7.4k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 5 months ago by ▴ 10 • written 2.0 years ago by ▴ 50
8
votes
2
replies
6.8k
views
handling outliers with DESeq2
RNASeqData DESeq2 Outliers
3.0 years ago paty ▴ 60
7
votes
5
replies
3.4k
views
Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
3.4 years ago ecg1g15 ▴ 20
6
votes
4
replies
11k
views
How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 2.3 years ago by • 0 • written 3.1 years ago by ▴ 10
5
votes
6
replies
530
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
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 ★ 1.3k • written 2.2 years ago by ▴ 10
4
votes
1
reply
2.4k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 2.1 years ago by 41k • written 2.1 years ago by ▴ 30
3
votes
4
replies
521
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
924
views
Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
3.2 years ago Wuschel ▴ 10
3
votes
3
replies
916
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
6
replies
1.3k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 3.4 years ago by 41k • written 3.4 years ago by ▴ 50
3
votes
2
replies
935
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 24 months ago Dakarai ▴ 10
3
votes
3
replies
1.4k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
23 months ago JK Kim ▴ 20
3
votes
5
replies
608
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 9 weeks ago by ▴ 10
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
6
replies
8.7k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
2.1 years ago treebig44 ▴ 30
3
votes
3
replies
1.2k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
7 months ago Ethan Nguyen • 0
3
votes
2
replies
666
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 10 months ago by 50k • written 10 months ago by ▴ 10
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
2
replies
394
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
5 months ago Manthos • 0
2
votes
1
reply
668
views
Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData DataImport oligo RNASeqData convert
updated 9 months ago by 65k • written 9 months ago by • 0
2
votes
3
replies
772
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 6 months ago by ★ 1.3k • written 6 months ago by • 0
2
votes
4
replies
661
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
2
votes
4
replies
2.8k
views
Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
3.4 years ago ecg1g15 ▴ 20
2
votes
9
replies
2.2k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
22 months ago Peipei • 0
2
votes
3
replies
1.4k
views
RNA-seq analysis without replicates
DESeq2 RESEQ RNASeqData
updated 12 months ago by • 0 • written 12 months ago by • 0
2
votes
3
replies
1.2k
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
24 months ago Maka • 0
2
votes
8
replies
2.3k
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
3
replies
1.1k
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 ★ 4.0k • written 10 months ago by ▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 10 days ago by • 0 • written 10 months ago by • 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 8 months ago by 65k • written 8 months ago by ▴ 10
1
vote
1
reply
394
views
Deseq contrast question
RNASeqData DESeq2
updated 10 months ago by 41k • written 10 months ago by ▴ 10
1
vote
1
reply
582
views
DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 10 months ago by ★ 4.0k • written 10 months ago by ▴ 10
1
vote
1
reply
448
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 9 months ago by 50k • written 9 months ago by • 0
1
vote
7
replies
819
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 4 months ago by 50k • written 6 months ago by • 0
1
vote
1
reply
640
views
Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 2.1 years ago by 41k • written 2.1 years ago by ▴ 30
1
vote
1
reply
754
views
NOIseq Probability column
RNAseq RNASeqData NOISeq
23 months ago • updated 22 months ago Pratibha ▴ 10
1
vote
1
reply
392
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
1
vote
1
reply
323
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
1
vote
1
reply
1.1k
views
Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 2.5 years ago by 50k • written 2.5 years ago by • 0
1
vote
2
replies
658
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
4 months ago Levi • 0
1
vote
6
replies
1.4k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
3.2 years ago Seaweed • 0
1
vote
2
replies
813
views
Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
2.1 years ago m.glymenaki • 0
1
vote
2
replies
659
views
Installation of R-packages for RNA-seq analysis
RNASeqData
14 months ago Begin-R • 0
1
vote
2
replies
2.5k
views
Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 20 months ago by ★ 1.3k • written 20 months ago by • 0
1
vote
4
replies
1.3k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2 Log2FC RNASeqData
15 months ago Iwan • 0
1
vote
1
reply
2.1k
views
Limma interaction term
RNASeqData limma DifferentialExpression
updated 2.1 years ago by 50k • written 2.1 years ago by • 0
1
vote
1
reply
781
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 2.2 years ago by 50k • written 2.2 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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