Showing : DGE • reset
5
votes
4
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1.3k
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 7.0 years ago by • 0 • written 7.0 years ago by ▴ 40
5
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6
replies
1.6k
views
How to calculate dispersion DESeq2 - Step by Step
DGE DESeq2 Differential
2.7 years ago Zeke Smith ▴ 10
3
votes
7
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2.2k
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How to determine the cause of no difference between treatments in rnaseq?
RNAseq DGE edger
updated 4.9 years ago by 50k • written 4.9 years ago by • 0
0
votes
4
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2.7k
views
edgeR DGEList and design matrix
edger DGE
updated 4.7 years ago by ▴ 840 • written 4.7 years ago by • 0
4
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8
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1.8k
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Advice regarding RNAseq data with no replicates, best approach to accomplish fold-change
rnaseq edger DGE no replicates
6.7 years ago Stefany Solano • 0
3
votes
8
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1.2k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 4.4 years ago by 65k • written 4.4 years ago by • 0
5
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10
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1.3k
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2 DGE contrast
updated 3.8 years ago by 41k • written 3.8 years ago by • 0
1
vote
2
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865
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How to construct matrix and fit linear model for this microarray?
microarray dge matrix makecontrasts limma
updated 3.8 years ago by 50k • written 3.8 years ago by ▴ 10
7
votes
6
replies
429
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
votes
1
reply
445
views
How to do PFS after Voom + Limma DGE ?
RNASeqData limma voom PFS DGE
updated 10 months ago by 65k • written 10 months ago by • 0
12
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10
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6.4k
views
edgeR glmLRT with test="F"?
edger dge differential expression
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ★ 7.9k
0
votes
3
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1.7k
views
glmQLFTest, coef=2:4, decideTestDGE not working
edger DGE coef
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
1
vote
5
replies
1.2k
views
edgeR or DESeq2 between duplicated chromosomes in the same individual
deseq2 edgeR normalization DGE
updated 4.5 years ago by 50k • written 4.5 years ago by ▴ 10
0
votes
2
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855
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Longitudinal Time-Course microarray experiment with two time points
edge DGE microarray
updated 4.5 years ago by 50k • written 4.5 years ago by • 0
0
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1
reply
1.5k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
3
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4
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1.9k
views
DGE matrix annotation
DGE DESeq2 AnnotationDbi
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
1
vote
3
replies
619
views
Can CAMERA analyze just one particular pathway
pathway ORA limma CAMERA DGE
updated 8 months ago by 50k • written 8 months ago by • 0
0
votes
3
replies
477
views
Deseq2, multifactor model design for comparing adult Mutant mouse versus pup Mutant mouse with normalization to the age difference of the Wildtype co…
DGE DESeq2
7 months ago ruba-mahmoud • 0
1
vote
1
reply
711
views
DESeq2 - DGE in organoids for multiple group comparisons
personalome organoids DGE DESeq2
updated 2.9 years ago by 41k • written 2.9 years ago by ▴ 10
0
votes
1
reply
795
views
DGE genes are not available in GSEA
dge gsea
updated 16 months ago by ★ 3.9k • written 16 months ago by • 0
0
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0
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896
views
quantifying piRNA and tRNA by Salmon
Salmon DGE
5.4 years ago lkianmehr • 0
21 results • Page 1 of 1
Recent ...
Replies
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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