4
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5
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13k
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[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 17 months ago by • 0 • written 8.2 years ago by ▴ 60
3
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4
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using limma trend workflow in CAMERA
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17 months ago • updated 16 months ago Jiahao Tian • 0
0
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0
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520
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Are equal whisker lengths important in an RLE plot?
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17 months ago BioinfGuru ▴ 70
0
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0
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761
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News: EuroBioC Updates: Important Deadlines
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17 months ago Maria Doyle ▴ 110
3
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
0
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2
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1.3k
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R is Removing the Gene Names in My Count Data
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updated 17 months ago by ▴ 70 • written 17 months ago by • 0
1
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4
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Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
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17 months ago • updated 16 months ago Bob ▴ 30
0
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1
reply
647
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Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2 NanoporeRNASeq DNASeq
updated 17 months ago by 43k • written 17 months ago by • 0
0
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2
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1.1k
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DMPs enrichment for MOUSE DNA methylation array
minfi mCSEA missme missMethyl
updated 16 months ago by • 0 • written 17 months ago by • 0
3
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3
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One-sided tests with CAMERA-PR
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updated 17 months ago by 53k • written 17 months ago by ▴ 10
0
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2
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FlowSOM library requires igraph but igraph does not install
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updated 8 months ago by • 0 • written 17 months ago by • 0
0
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2
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539
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get_snp
frmaTools
updated 17 months ago by 68k • written 17 months ago by • 0
0
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0
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588
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hichip fragments extraction chip seq
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17 months ago user_bioinfo • 0
0
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3
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1.1k
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comparing common differentially expressed genes from two Rna-Seq Dataset.
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written 17 months ago by • 0
3
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5
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2.5k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
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updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
2
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1
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1.7k
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DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
0
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1
reply
649
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DiffBind remove Unplace Chromosome (chrUn)
DiffBind
17 months ago mdidish ▴ 10
0
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0
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551
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DiffBind dba.plotprofile y-axis range
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17 months ago Tara • 0
2
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4
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887
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Bioconductor Submission question
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17 months ago XFWu • 0
2
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3
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1.4k
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RUV - Does my data need further normalisation?
EDASeq plotRLE RNAseq
17 months ago BioinfGuru ▴ 70
2
votes
2
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918
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Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
17 months ago BioinfGuru ▴ 70
0
votes
0
replies
486
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proActiv-promoter analysis
proActiv Transcriptomics
17 months ago wang.xiangyu • 0
2
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1
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2.4k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 17 months ago by ★ 29k • written 17 months ago by • 0
0
votes
0
replies
583
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News: Annual Nominations Open for CAB and TAB! Deadline Aug 31
TAB CAB Bioconductor
17 months ago shepherl 4.3k
1
vote
2
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822
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Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
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17 months ago DL • 0
0
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3
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744
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How to combine multiple lists of cytoframes/cytocq data objects into one
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updated 17 months ago by ▴ 360 • written 17 months ago by ▴ 30
0
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1
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845
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edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 17 months ago by 53k • written 17 months ago by • 0
1
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4
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How to Query Only SNPs from the biomaRt Variation Database
biomaRt
17 months ago kschecht • 0
0
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1
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1.2k
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Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea GSVA gsea
updated 17 months ago by ★ 1.1k • written 17 months ago by • 0
0
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0
replies
581
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EuroBioC2024 Flashtalks & Birds-of-a-Feather Sessions - submissions open!
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17 months ago Maria Doyle ▴ 110
0
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1
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728
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Is CEMiTool for gene coexpression analysis suitable for single cell RNA Seq data?
SingleCellData CEMiTool
updated 17 months ago by 68k • written 17 months ago by • 0
3
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3
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Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 17 months ago by 68k • written 17 months ago by ▴ 60
2
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3
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958
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EBImage Rendering of a DelayedArray Object
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updated 8 months ago by 16k • written 17 months ago by ★ 1.6k
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3
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makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
17 months ago Anna • 0
0
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3
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950
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RNA-seq with DESeq2 shrinkage estimation
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updated 17 months ago by 68k • written 17 months ago by • 0
0
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4
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featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
18 months ago • updated 17 months ago Jessica • 0
2
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8
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biomaRt getLDS error
biomaRt
17 months ago mark.dunning ▴ 20
1
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2
replies
907
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Question on number of genes used in GO analysis
GO clusterProfiler
17 months ago Danté • 0
6
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15
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2.7k
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Deseq2 design formula and analysis with internal controls
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updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
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4
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Failed to install geneLenDataBase
geneLenDataBase ChAMP
updated 17 months ago by 4.3k • written 17 months ago by • 0
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4
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WTChimeraData() Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [experimenthub.bioconductor.org] Connection time-out
WTChimeraData MouseGastrulationData WT
17 months ago haidan • 0
1
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2
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1.4k
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
17 months ago grothmn • 0
4
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4
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1.8k
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NAs in fgseaMultilevel
fgsea
updated 17 months ago by ▴ 280 • written 17 months ago by • 0
1
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2
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982
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mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
17 months ago Anke • 0
0
votes
8
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1.5k
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DiffBind full library size not reliable
DiffBind Reads MACS2 FullLibSize
updated 17 months ago by ★ 5.2k • written 17 months ago by ▴ 20
1
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1
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1.1k
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biomaRt getSequence(): Error in .lock2
ensembldb getSequence
updated 17 months ago by ★ 6.6k • written 17 months ago by ▴ 10
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2
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1.8k
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save.rnb.set warnings when trying to save rnb.set
RnBeads RnBeads.hg19 MethylationArray
updated 6 months ago by • 0 • written 17 months ago by • 0
0
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5
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1.2k
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preprocessENmix colnames Error
ENmix Preprocessing
17 months ago Eve • 0
0
votes
1
reply
1.3k
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HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 17 months ago by 68k • written 17 months ago by • 0
4
votes
7
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2.4k
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What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 17 months ago by ▴ 10 • written 18 months ago by ▴ 70
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Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
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Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
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Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
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