2
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13
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434
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Trying to use enrichGO
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17 days ago • updated 13 days ago fernanda.backsouza ▴ 10
5
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6
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433
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Not fully paired differential gene expression analysis
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updated 25 days ago by ★ 4.1k • written 29 days ago by ▴ 30
0
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7
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426
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DESeq filtering specific to contrasts
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updated 19 days ago by 42k • written 11 weeks ago by • 0
2
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6
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410
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
4 weeks ago • updated 29 days ago Chris • 0
2
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9
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397
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 12 days ago by 65k • written 13 days ago by • 0
2
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2
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392
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
26 days ago Henry ▴ 10
0
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8
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356
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 13 days ago by ★ 1.3k • written 15 days ago by • 0
1
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3
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352
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Why is my gene not significantly differentially expressed?
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updated 23 days ago by 50k • written 28 days ago by • 0
0
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1
reply
346
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Gene names from Matrix
BioCor StarBioTrek MatrixGenerics
updated 28 days ago by ▴ 730 • written 7 months ago by • 0
0
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6
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343
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unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 27 days ago by ▴ 180 • written 5 weeks ago by • 0
3
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3
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343
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permutation test in edgeR
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updated 17 days ago by 50k • written 4 weeks ago by • 0
1
vote
2
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342
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 4 days ago by 50k • written 4 days ago by • 0
1
vote
4
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339
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
14 days ago • updated 12 days ago winwater0928 • 0
1
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7
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333
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Math expression in shapeCustom legend in EnhancedVolcano
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13 days ago • updated 12 days ago pl23 • 0
2
votes
3
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329
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ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
23 days ago • updated 22 days ago daniel.carbajo • 0
0
votes
7
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325
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Methylation Analysis experiment design using Limma
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21 days ago • updated 15 days ago hortense96 • 0
3
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1
reply
316
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 14 days ago by 42k • written 14 days ago by ▴ 40
1
vote
2
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313
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CombineArrays for EPIC and EPIC V2
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4 weeks ago • updated 4 days ago Kim • 0
0
votes
5
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304
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Error for AnnotationForge makeOrgPackageFromNCBI function
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updated 14 days ago by 65k • written 16 days ago by • 0
1
vote
0
replies
293
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Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
19 days ago BioinfGuru ▴ 30
3
votes
4
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281
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 6 hours ago by ★ 6.5k • written 2 days ago by • 0
3
votes
6
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281
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Surrogate variable analysis for paired RNA seq experiment
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27 days ago nhaus ▴ 30
2
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5
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276
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get BM error
ensembldb
updated 14 days ago by 65k • written 14 days ago by • 0
0
votes
4
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272
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DEG with low counts
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updated 19 days ago by 42k • written 23 days ago by • 0
0
votes
3
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263
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A ComBat-seq issue: the covariates are confounded
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updated 20 days ago by ▴ 850 • written 26 days ago by • 0
0
votes
3
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260
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 6 days ago by 42k • written 7 days ago by • 0
0
votes
2
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259
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
5 weeks ago • updated 19 days ago isaac.vock • 0
0
votes
2
replies
252
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featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
15 days ago • updated 13 days ago shuwangxinze1996 • 0
0
votes
4
replies
250
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Minfi - estimatecellscount
min minfi
updated 9 days ago by 65k • written 5 weeks ago by • 0
0
votes
2
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249
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Regressing out batch effects
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updated 28 days ago by 42k • written 4 weeks ago by • 0
2
votes
5
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248
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How to retrieve gene ontology GO class from gene list?
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updated 13 days ago by 65k • written 14 days ago by • 0
0
votes
3
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247
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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 8 days ago by 65k • written 9 days ago by • 0
1
vote
2
replies
245
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How to retrieve detailed regression results from deseq2
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27 days ago • updated 18 days ago Weiqian ▴ 10
0
votes
4
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242
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Differential peaks that were not identified in diffbind were identified in diseq2
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21 days ago • updated 18 days ago lonn • 0
1
vote
2
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241
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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7 days ago • updated 6 days ago Yveto • 0
1
vote
4
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241
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Error EPICv2 ChAMP
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updated 16 days ago by 65k • written 20 days ago by • 0
3
votes
3
replies
241
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 9 days ago by ★ 4.1k • written 9 days ago by ▴ 10
1
vote
3
replies
235
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 10 hours ago by ★ 4.1k • written 6 days ago by • 0
1
vote
0
replies
234
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News: Nominations for Bioconductor Awards 2024!
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6 weeks ago • updated 1 day ago shepherl 3.9k
0
votes
1
reply
234
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 7 days ago by 65k • written 8 days ago by • 0
3
votes
3
replies
231
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 15 days ago by 42k • written 16 days ago by • 0
0
votes
4
replies
230
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Storing directories inside an ExperimentHub package?
ExperimentHub
28 days ago • updated 26 days ago Tim Barry • 0
0
votes
6
replies
228
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Once again a "Model matrix not full rank"
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updated 4 days ago by ★ 1.3k • written 5 days ago by ▴ 130
1
vote
3
replies
227
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 12 days ago by 42k • written 12 days ago by • 0
0
votes
2
replies
223
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Interaction term vs grouping variable design considerations
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updated 28 days ago by 42k • written 4 weeks ago by ▴ 30
3
votes
4
replies
223
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Help with error using camera() in limma
CAMERA limma
8 days ago • updated 7 days ago Chris • 0
1
vote
2
replies
221
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significant difference of p-values with dream() after updating VariancePartition
variancePartition
20 days ago • updated 19 days ago Le • 0
3
votes
2
replies
219
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Cannabis and KEGGgraph
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updated 16 days ago by ★ 3.9k • written 18 days ago by ▴ 10
1
vote
3
replies
217
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Different Shrunk Log2FC according with reference
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updated 14 days ago by 42k • written 14 days ago by ▴ 20
3
votes
3
replies
215
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Reading huge bismark coverage files using bbseq::read.bismark
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26 days ago • updated 20 days ago jacques.imbert • 0
201 results • Page 2 of 5
Recent ...
Replies
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results by ATpoint ★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
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: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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