1
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4
replies
360
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
26 days ago • updated 24 days ago winwater0928 • 0
1
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0
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335
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News: Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
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8 weeks ago • updated 5 days ago shepherl 3.9k
4
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5
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334
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Method to find pathways different between 2 groups
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14 days ago • updated 4 days ago Chris ▴ 10
3
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1
reply
329
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 26 days ago by 42k • written 26 days ago by ▴ 40
0
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5
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325
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Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 25 days ago by 65k • written 28 days ago by • 0
5
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3
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317
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Log-cpm values from limma
limma edgeR RNASeq
updated 10 days ago by 50k • written 4 weeks ago by • 0
2
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5
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313
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get BM error
ensembldb
updated 25 days ago by 65k • written 26 days ago by • 0
1
vote
3
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305
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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 12 days ago by ★ 4.1k • written 18 days ago by • 0
3
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5
replies
302
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Help with running egsea()
EGSEA
13 days ago • updated 12 days ago Chris ▴ 10
0
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6
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302
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Once again a "Model matrix not full rank"
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updated 16 days ago by ★ 1.4k • written 17 days ago by ▴ 130
0
votes
3
replies
302
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 18 days ago by 42k • written 19 days ago by • 0
1
vote
2
replies
294
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
19 days ago • updated 18 days ago Yveto • 0
3
votes
4
replies
289
views
Store output of matchPWM()
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18 days ago • updated 6 days ago mat149 ▴ 70
2
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4
replies
287
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 27 days ago by 65k • written 4 weeks ago by • 0
2
votes
2
replies
285
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
12 days ago • updated 7 days ago zzrammal • 0
0
votes
3
replies
282
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 19 days ago by 65k • written 20 days ago by • 0
1
vote
2
replies
280
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
11 days ago • updated 10 days ago Dylan.Sheerin • 0
2
votes
3
replies
277
views
package goseq seems to be not available on the latest version of R
goseq
updated 14 days ago by 50k • written 16 days ago by ▴ 20
3
votes
3
replies
271
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 21 days ago by ★ 4.1k • written 21 days ago by ▴ 10
0
votes
2
replies
268
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
27 days ago • updated 25 days ago shuwangxinze1996 • 0
0
votes
1
reply
266
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 19 days ago by 65k • written 20 days ago by • 0
3
votes
4
replies
266
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Help with error using camera() in limma
CAMERA limma
19 days ago Chris ▴ 10
0
votes
4
replies
265
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Minfi - estimatecellscount
min minfi
updated 20 days ago by 65k • written 7 weeks ago by • 0
4
votes
9
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264
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Can DESeq2 rlog normalized matrix reflects time course result directly?
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updated 4 days ago by ★ 4.1k • written 5 days ago by • 0
2
votes
5
replies
259
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How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 24 days ago by 65k • written 26 days ago by • 0
2
votes
3
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257
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Too many significant genes when integrating gtex and tcga
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updated 15 days ago by ★ 4.1k • written 16 days ago by • 0
1
vote
3
replies
255
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 24 days ago by 42k • written 24 days ago by • 0
1
vote
3
replies
254
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 5 days ago by 50k • written 6 days ago by • 0
3
votes
3
replies
253
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 27 days ago by 42k • written 27 days ago by • 0
1
vote
2
replies
249
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
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6 days ago • updated 3 days ago BioinfGuru ▴ 30
0
votes
2
replies
245
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RNAseq:Technical replicates from different batches
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4 weeks ago • updated 28 days ago catv • 0
2
votes
2
replies
238
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
20 days ago Chris ▴ 10
1
vote
3
replies
238
views
Different Shrunk Log2FC according with reference
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updated 26 days ago by 42k • written 26 days ago by ▴ 20
3
votes
2
replies
238
views
Cannabis and KEGGgraph
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updated 28 days ago by ★ 4.0k • written 4 weeks ago by ▴ 10
1
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4
replies
233
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minfi::read.metharray.exp
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updated 26 days ago by ▴ 780 • written 27 days ago by • 0
0
votes
3
replies
233
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Couldn't connect to server while using "pathways"
graphite
updated 13 days ago by 42k • written 14 days ago by • 0
2
votes
2
replies
232
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fgsea significant result
fgsea
15 days ago • updated 14 days ago Chris ▴ 10
0
votes
2
replies
229
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PCA plot suggestions
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updated 23 days ago by 42k • written 25 days ago by • 0
0
votes
3
replies
227
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Differences in differential analysis methods for RNA-Seq
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updated 18 days ago by ★ 4.1k • written 18 days ago by • 0
2
votes
5
replies
222
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Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db Bioconductor
4 days ago • updated 3 days ago Patadù ▴ 10
1
vote
2
replies
216
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Improving the design matrices vignette in RNAseq123
RNAseq123
28 days ago • updated 14 days ago Lluís Revilla Sancho ▴ 730
0
votes
2
replies
215
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Deseq2 and Normalization of RNA sequencing data
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18 days ago • updated 17 days ago kcarey • 0
1
vote
2
replies
205
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Citation for edgeR user guide
edgeR
written 26 days ago by ▴ 30
1
vote
1
reply
193
views
Handling multiple differential expression comparisons
DESeq2
updated 15 days ago by 42k • written 16 days ago by ▴ 10
0
votes
2
replies
192
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 27 days ago by • 0
0
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3
replies
190
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 19 days ago by ★ 1.9k • written 4 weeks ago by • 0
0
votes
3
replies
188
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ChAMP installation issue
Cha ChAMP
7 days ago • updated 6 days ago e1271094 • 0
2
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1
reply
181
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minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 13 days ago by 65k • written 13 days ago by • 0
0
votes
1
reply
179
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 17 days ago by 50k • written 17 days ago by • 0
0
votes
1
reply
178
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Differential gene expression analysis results
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updated 10 days ago by ★ 4.1k • written 10 days ago by • 0
169 results • Page 2 of 4
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
edgeR used a prior count which stabilizes LFC while DESeq2 does not. Note that the SE are larger in these cases so you don't have experime…
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
Good day ATpoint, Could you pls advise also ehy this error could happened design contains one or more variables with all samples having t…
Comment: How to run allelic imbalance in apeglm by euge.eugenio ▴ 20
@mikelove could you help me? Thanks!
Comment: ENCORI or starBase : ceRNA data retrieval using Web API and curl by ATpoint ★ 4.1k
This is not related to Bioconductor. Biostars is more suited where you posted already.
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Votes
biomaRt not working - lazy table error
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: 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
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