5
votes
3
replies
313
views
Log-cpm values from limma
limma edgeR RNASeq
updated 9 days ago by 50k • written 4 weeks ago by • 0
1
vote
3
replies
236
views
Different Shrunk Log2FC according with reference
DESeq2
updated 25 days ago by 42k • written 25 days ago by ▴ 20
0
votes
3
replies
180
views
ChAMP installation issue
Cha ChAMP
6 days ago • updated 5 days ago e1271094 • 0
2
votes
3
replies
1.8k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 6 days ago by • 0 • written 3.6 years ago by ▴ 60
3
votes
3
replies
271
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 20 days ago by ★ 4.1k • written 20 days ago by ▴ 10
0
votes
3
replies
101
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 2 days ago by ▴ 80 • written 2 days ago by • 0
0
votes
3
replies
8.9k
views
SingleR Label.Ont
SingleR
updated 8 days ago by • 0 • written 8 months ago by • 0
0
votes
3
replies
225
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 17 days ago by ★ 4.1k • written 17 days ago by • 0
0
votes
3
replies
280
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
3
replies
248
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 4 days ago by 50k • written 5 days ago by • 0
0
votes
3
replies
233
views
Couldn't connect to server while using "pathways"
graphite
updated 13 days ago by 42k • written 13 days ago by • 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz Mfuzz
updated 13 days ago by • 0 • written 13.1 years ago by ▴ 720
1
vote
3
replies
891
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 25 days ago by ★ 1.2k • written 14 months ago by ▴ 10
2
votes
3
replies
124
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 3 days ago by 50k • written 4 days ago by • 0
1
vote
3
replies
305
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 11 days ago by ★ 4.1k • written 18 days ago by • 0
2
votes
3
replies
104
views
Problem installing ChAMP on a MacBook
ChAMP
updated 3 days ago by 3.9k • written 3 days ago by • 0
0
votes
3
replies
302
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 17 days ago by 42k • written 18 days ago by • 0
1
vote
3
replies
255
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 23 days ago by 42k • written 24 days ago by • 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 19 days ago by • 0 • written 13.1 years ago by ▴ 10
3
votes
3
replies
368
views
permutation test in edgeR
rna-seq edgeR
updated 28 days ago by 50k • written 5 weeks ago by • 0
2
votes
3
replies
273
views
package goseq seems to be not available on the latest version of R
goseq
updated 13 days ago by 50k • written 16 days ago by ▴ 20
3
votes
3
replies
253
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 26 days ago by 42k • written 27 days ago by • 0
0
votes
3
replies
189
views
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
2.1k
views
maSigPro genes from clusters
masigpro clustering
updated 2 days ago by • 0 • written 7.9 years ago by • 0
0
votes
2
replies
103
views
Problem finding certain variables when importing a public database GSE73103
GSEABase GenomicDistributionsData
6 days ago • updated 5 days ago Yveto • 0
0
votes
2
replies
819
views
Job: Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor artificialintelligence JobPosting machinelearning
written 8 months ago by 50k
1
vote
2
replies
375
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
6 weeks ago • updated 15 days ago Kim • 0
0
votes
2
replies
191
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 26 days ago by • 0
1
vote
2
replies
407
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 15 days ago by 50k • written 15 days ago by • 0
0
votes
2
replies
170
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
19 days ago • updated 16 days ago Aurora • 0
0
votes
2
replies
241
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
4 weeks ago • updated 27 days ago catv • 0
0
votes
2
replies
950
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 4 days ago by • 0 • written 18 months ago by • 0
4
votes
2
replies
629
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
17 days ago • updated 13 days ago gene_bioconductor ▴ 10
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 9 days ago by • 0 • written 16 months 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
26 days ago • updated 24 days ago shuwangxinze1996 • 0
0
votes
2
replies
166
views
DESeq2 v1.35.0
DESeq2
updated 17 days ago by 42k • written 17 days ago by • 0
3
votes
2
replies
234
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 27 days ago by ★ 4.0k • written 29 days ago by ▴ 10
1
vote
2
replies
177
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
25 days ago • updated 24 days ago ATpoint ★ 4.1k
2
votes
2
replies
382
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
7 days ago • updated 3 days ago Matthew Thornton ▴ 360
0
votes
2
replies
229
views
PCA plot suggestions
DESeq2 PCAtools
updated 23 days ago by 42k • written 24 days ago by • 0
2
votes
2
replies
238
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
20 days ago Chris ▴ 10
0
votes
2
replies
130
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 5 days ago by ▴ 10 • written 7 days ago by • 0
1
vote
2
replies
128
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
5 days ago • updated 4 days ago Daniel • 0
1
vote
2
replies
293
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
18 days ago • updated 17 days ago Yveto • 0
1
vote
2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate Gviz
updated 26 days ago by ▴ 180 • written 14 months ago by ▴ 10
0
votes
2
replies
110
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
3 days ago makala • 0
1
vote
2
replies
243
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
5 days ago • updated 3 days ago BioinfGuru ▴ 30
0
votes
2
replies
752
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 3 days ago by • 0 • written 11 months ago by • 0
0
votes
2
replies
111
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 1 day ago by 42k • written 2 days ago by • 0
1
vote
2
replies
95
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
4 days ago Patadù ▴ 10
168 results • Page 2 of 4
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
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
Awards • All
Popular Question to euge.eugenio ▴ 20
Popular Question to Dario Strbenac ★ 1.5k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Locations • All
Germany, 6 minutes ago
United States, 15 minutes ago
Poland, 17 minutes ago
Germany, 18 minutes ago
United States, 21 minutes ago
Traffic: 353 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6