Showing : DIfferential expression • reset
3
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4
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3.7k
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Protein differential Expression analysis
differential expression proteomics
updated 19 months ago by ★ 4.8k • written 7.2 years ago by • 0
0
votes
17
replies
4.3k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 21 months ago by • 0 • written 7.5 years ago by • 0
3
votes
3
replies
4.3k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.0 years ago by ▴ 30 • written 6.2 years ago by ▴ 40
4
votes
2
replies
2.1k
views
Moderated F-test followed by moderated t-test in limma
limma differential expression
updated 4.6 years ago by 52k • written 4.6 years ago by • 0
5
votes
3
replies
1.8k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 20
3
votes
1
reply
1.4k
views
Obtain p-values for group * condition interaction using DESeq2?
DESeq2 interaction differential expression
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 180
6
votes
7
replies
3.4k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
updated 12 weeks ago by 52k • written 4.9 years ago by ▴ 20
1
vote
1
reply
2.1k
views
Differential expression on Nanostring normalised protein data
R Differential expression
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
0
votes
4
replies
1.7k
views
Agilent two-color microarray analysis with limma: 2x3 factorial design
limma microarray contrast matrix 2x3 factorial design differential expression
updated 4.9 years ago by 52k • written 5.0 years ago by • 0
2
votes
2
replies
938
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edgeR - Correct approach to compare abundances of genomic regions?
edger differential expression
updated 5.0 years ago by 52k • written 5.0 years ago by ▴ 20
0
votes
0
replies
920
views
Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
5.0 years ago raquelponti • 0
0
votes
1
reply
881
views
using deseq2 for intronic counts for 2 conditins with replicates
deseq2 intron differential expression
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 40
4
votes
7
replies
1.6k
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 60
7
votes
4
replies
6.2k
views
Limma when to use zero intercept
limma regression differential expression linear model
updated 5.1 years ago by 52k • written 5.1 years ago by • 0
2
votes
1
reply
807
views
Detecting the power in differential expression
POWER DESEQ2 edger LIMMA DIfferential expression
5.4 years ago • updated 5.3 years ago Beginner • 0
2
votes
3
replies
1.7k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 180
0
votes
1
reply
1.1k
views
How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
5.4 years ago A • 0
0
votes
0
replies
1.8k
views
GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
5.4 years ago fawazfebin ▴ 60
9
votes
11
replies
3.2k
views
dream vignette says limma-voom repeated measures two-group comparison needs two duplicateCorrelation rounds which differs from limma user's guide and…
dream variancePartition limma differential expression repeated measures
updated 5.5 years ago by 52k • written 5.5 years ago by ▴ 20
5
votes
8
replies
2.3k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 5.5 years ago by ★ 13k • written 5.5 years ago by ▴ 30
3
votes
2
replies
2.4k
views
Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
5
votes
6
replies
1.7k
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 5.6 years ago by ▴ 900 • written 5.6 years ago by ▴ 10
0
votes
1
reply
2.3k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
5.6 years ago Andrew_McDavid ▴ 270
27
votes
17
replies
9.0k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 3.8 years ago by 43k • written 6.8 years ago by ▴ 50
2
votes
4
replies
1.7k
views
Majority upregulated genes in edgeR
edger differential expression genes fold change
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
1
vote
1
reply
1.2k
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2 differential expression batch correction design
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 40
4
votes
4
replies
1.8k
views
Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 40
1
vote
12
replies
1.8k
views
RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 5.8 years ago by 52k • written 5.8 years ago by ▴ 90
4
votes
5
replies
5.4k
views
How does limma calculate the log2fc?
Limma Differential Expression Time-course Analysis
updated 5.9 years ago by 52k • written 5.9 years ago by ▴ 10
1
vote
1
reply
1.2k
views
How to normalize RNA-seq when 50% genes are DE? (TMM)
limma TMM differential expression normalization rnaseq
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
0
votes
1
reply
1.3k
views
Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
Scran MNN_correct Differential expression single-cell
6.0 years ago baldissera152 • 0
5
votes
1
reply
1.5k
views
Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
0
votes
3
replies
1.9k
views
How to handle replicates and treatment conditions in TissueEnrich package
rna-seq TissueEnrich tissue-specific expression differential expression
updated 6.2 years ago by ▴ 10 • written 6.2 years ago by • 0
1
vote
1
reply
1.6k
views
PLAGE method fails in GSVA if an overlap between gene sets and genes in expressions is less than two
gsva plage differential expression gene set enrichment
6.2 years ago krassowski.michal ▴ 40
2
votes
7
replies
2.7k
views
Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 6.6 years ago by 52k • written 6.6 years ago by • 0
15
votes
12
replies
3.0k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 ZINB-WaVE single cell RNA-seq differential expression
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 60
2
votes
3
replies
1.9k
views
Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 6.7 years ago by ▴ 980 • written 6.7 years ago by • 0
1
vote
4
replies
1.9k
views
venDiagram after limma showing more genes after specifying up or down regulated specifically
venn diagram venndiagram limma microarray differential expression
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 60
5
votes
1
reply
1.3k
views
DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
0
votes
4
replies
1.8k
views
Deseq2 problem visualizing gene expression with batch corrected values
deseq2 limma differential expression visualization
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
1
vote
4
replies
1.6k
views
DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
deseq2 sequence length normalization RSEM tximport differential expression
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 50
0
votes
0
replies
1.2k
views
pair wise ballgown
ballgown differential expression
6.8 years ago zoe.ward • 0
0
votes
0
replies
1.5k
views
Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
6.8 years ago manuelmendoza • 0
1
vote
6
replies
1.6k
views
differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
6.9 years ago aec ▴ 90
0
votes
1
reply
1.2k
views
Interpretation of p-value plot
p values differential expression limma
updated 6.9 years ago by 52k • written 6.9 years ago by • 0
5
votes
4
replies
1.5k
views
Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 6.9 years ago by 52k • written 6.9 years ago by • 0
0
votes
3
replies
1.1k
views
interaction model deseq2 specific DE genes
deseq2 interaction model differential expression
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 90
6
votes
4
replies
1.8k
views
Fitting Gamma GLMs for examining differential expression
deseq2 edger differential expression
updated 7.0 years ago by ★ 7.9k • written 7.0 years ago by ▴ 10
7
votes
10
replies
7.0k
views
Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 7.0 years ago by ▴ 30 • written 8.7 years ago by ▴ 50
7
votes
11
replies
3.0k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 7.1 years ago by 52k • written 7.1 years ago by ▴ 60
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Comment: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Arctic • 0
Many thanks for the link to the C++ code. I will see if I can find someone with C++ experience to help me with the code breakdown from her…
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Aaron Lun ★ 28k
It's calling C++ code, see the relevant function definitions on [GitHub](https://github.com/knncolle/BiocNeighbors/blob/master/src/generics…
Answer: DESeq2 by ATpoint ★ 4.8k
Time courses are often inevitable batches but you should have done the library prep at the same day, just extract RNA per day. If not then …
Comment: Package developing and interoperation with Bioconductor by slizchap • 0
Thank you so much for your answer. This was very useful, I will optimize my functions so they can handle SE objects.
Comment: Package developing and interoperation with Bioconductor by slizchap • 0
Thank you so much for your answer, very useful!
Votes
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin
Comment: ComBat with repeated measures
Answer: Package developing and interoperation with Bioconductor
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