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418
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Not fully paired differential gene expression analysis
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16 days ago • updated 11 days ago Jonathan ▴ 10
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25 days ago Chris • 0
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Trying to use enrichGO
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
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22 days ago • updated 21 days ago Henry ▴ 10
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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updated 8 days ago by 65k • written 8 days ago by • 0
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Why is my gene not significantly differentially expressed?
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updated 18 days ago by 50k • written 23 days ago by • 0
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Gene names from Matrix
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DESeq2 output used for PCA plot on R studio
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updated 8 days ago by ★ 1.3k • written 10 days ago by • 0
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unable to access Annotationhub latest record
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updated 22 days ago by ▴ 180 • written 4 weeks ago by • 0
3
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permutation test in edgeR
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updated 12 days ago by 50k • written 25 days ago by • 0
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ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
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18 days ago • updated 17 days ago daniel.carbajo • 0
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Opposite sign of LFC in count plots of DEGs (DESeq2)
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9 days ago • updated 7 days ago winwater0928 • 0
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Help with design.matrix
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Math expression in shapeCustom legend in EnhancedVolcano
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8 days ago • updated 7 days ago pl23 • 0
3
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
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updated 9 days ago by 41k • written 10 days ago by ▴ 40
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Methylation Analysis experiment design using Limma
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16 days ago • updated 10 days ago hortense96 • 0
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Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
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4 weeks ago • updated 28 days ago fer_talavera • 0
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22 days ago nhaus ▴ 30
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updated 14 days ago by 41k • written 19 days ago by • 0
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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4 weeks ago • updated 14 days ago isaac.vock • 0
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CombineArrays for EPIC and EPIC V2
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4 weeks ago • updated 1 hour ago Kim • 0
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2
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get BM error
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updated 9 days ago by 65k • written 9 days ago by • 0
1
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updated 27 days ago by 65k • written 28 days ago by • 0
1
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22 days ago • updated 14 days ago Weiqian ▴ 10
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updated 23 days ago by 41k • written 29 days ago by • 0
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updated 2 days ago by 41k • written 3 days ago by • 0
1
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updated 28 days ago by 65k • written 4 weeks ago by • 0
2
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updated 8 days ago by 65k • written 10 days ago by • 0
1
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Error EPICv2 ChAMP
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updated 11 days ago by 65k • written 15 days ago by • 0
0
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4
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220
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Storing directories inside an ExperimentHub package?
ExperimentHub
23 days ago • updated 22 days ago Tim Barry • 0
3
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3
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218
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updated 10 days ago by 41k • written 11 days ago by • 0
0
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2
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215
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updated 23 days ago by 41k • written 28 days ago by ▴ 30
0
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
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updated 3 days ago by 65k • written 4 days ago by • 0
0
votes
1
reply
211
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
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updated 3 days ago by 65k • written 3 days ago by • 0
1
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2
replies
209
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significant difference of p-values with dream() after updating VariancePartition
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15 days ago Le • 0
3
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2
replies
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Cannabis and KEGGgraph
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updated 11 days ago by ★ 3.9k • written 14 days ago by ▴ 10
1
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updated 9 days ago by 41k • written 9 days ago by ▴ 20
0
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3
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202
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updated 17 days ago by 41k • written 18 days ago by ▴ 20
0
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2
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14 days ago • updated 11 days ago catv • 0
0
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201
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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2 days ago • updated 1 day ago Yveto • 0
3
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3
replies
201
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
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updated 4 days ago by ★ 4.1k • written 4 days ago by ▴ 10
205 results • Page 2 of 5
Recent ...
Replies
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Votes
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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