0
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2
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193
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 15 days ago by 41k • written 20 days ago by ▴ 30
0
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1
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141
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 15 days ago by 41k • written 15 days ago by • 0
0
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2
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222
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Regressing out batch effects
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5
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6
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393
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edgeR DifferentialExpression
updated 12 days ago by ★ 4.0k • written 16 days ago by ▴ 30
0
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1
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129
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BAM write error in HTSeqGenie
HTSeqGenie BAM
updated 15 days ago by 65k • written 15 days ago by • 0
1
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6
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454
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GSVA on separate healthy and disease datasets
GSVA
updated 15 days ago by 65k • written 16 days ago by ▴ 60
0
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0
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91
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ggtree tip label position (depth)
ggtree
16 days ago • updated 15 days ago Roope • 0
2
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6
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345
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How to make boxplot with pairwise and overall p value from Limma
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16 days ago Chris • 0
0
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1
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159
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How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
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updated 17 days ago by 65k • written 17 days ago by • 0
0
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0
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122
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Job: PhD-position in bioinformatics / computational biology
Mergeomics Epigenome Evolution NGS Aging
17 days ago arne.sahm • 0
0
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0
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84
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News: Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry conference
17 days ago Wolfgang Huber ★ 13k
1
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10
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404
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Obtaining pheno data from CEL files
GEO affy
23 days ago • updated 16 days ago Kurtis • 0
0
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1
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145
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Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 19 days ago by 50k • written 19 days ago by • 0
1
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3
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228
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 19 days ago by 65k • written 20 days ago by • 0
1
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2
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201
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methylKit
updated 19 days ago by 65k • written 24 days ago by • 0
1
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2
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3.1k
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ggvenn
updated 19 days ago by ▴ 10 • written 24 months ago by • 0
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4
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290
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limma
19 days ago • updated 18 days ago andrea.rodriguez-martinez13 • 0
0
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0
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134
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Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
20 days ago • updated 19 days ago andromeda • 0
0
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2
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143
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 20 days ago by 65k • written 20 days ago by • 0
2
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2
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170
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Bluster and Varieties of Louvain Clulstering
bluster
updated 20 days ago by ★ 4.0k • written 20 days ago by ★ 1.5k
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1
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117
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Granges regionCounts not returning the expected number of entries
methylKit
20 days ago • updated 19 days ago Modoc Kesner ▴ 10
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0
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85
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flowDensity on a flowset
flowDensity
20 days ago fredrikwallberg • 0
1
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1
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153
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DESeq2 - Missing values in count matrix
DESeq2
updated 21 days ago by 65k • written 21 days ago by • 0
7
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36
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5.5k
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Ensembl plants at annotationHub?
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updated 21 days ago by • 0 • written 5.4 years ago by ★ 3.9k
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1
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214
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CombineArrays for EPIC and EPIC V2
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updated 21 days ago by ▴ 170 • written 21 days ago by • 0
0
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0
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DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
21 days ago Macsue • 0
1
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4
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413
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 20 days ago by 50k • written 22 days ago by • 0
3
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3
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13k
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How to fix 'long vectors not supported yet' error in R
r
updated 21 days ago by • 0 • written 5.2 years ago by • 0
0
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2
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739
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error in install immunedeconv
Install
updated 21 days ago by • 0 • written 13 months ago by • 0
1
vote
6
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403
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 21 days ago by 41k • written 21 days ago by • 0
0
votes
2
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172
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
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22 days ago • updated 21 days ago Gimena • 0
0
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2
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146
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
22 days ago Marianna ▴ 20
2
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6
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How to get DMR for Infinium methylation EPIC v2
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updated 22 days ago by ▴ 170 • written 5 months ago by ▴ 10
0
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6
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307
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unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 14 days ago by ▴ 170 • written 23 days ago by • 0
1
vote
1
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138
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
23 days ago • updated 22 days ago Layal • 0
0
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2
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213
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
28 days ago • updated 23 days ago w.cookson • 0
0
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2
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153
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
23 days ago • updated 22 days ago michelafrancesconi8 • 0
0
votes
1
reply
125
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Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 23 days ago by 65k • written 23 days ago by • 0
0
votes
4
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232
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by 41k • written 23 days ago by • 0
0
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4
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392
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
24 days ago • updated 23 days ago Lucy ▴ 60
0
votes
1
reply
97
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Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 23 days ago by 65k • written 24 days ago by • 0
0
votes
2
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166
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How to make GSEAplot with chip set
geneset GeneSetEnrichment msigdb
24 days ago • updated 23 days ago Seongsu • 0
0
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2
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165
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Gene Ontology doubt
microbiomeExplorer
24 days ago • updated 20 days ago Bhawna • 0
0
votes
1
reply
156
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Convert transcriptomic bam to genomic bam?
ensembldb transcriptome genome coordinateconversion
updated 24 days ago by 41k • written 26 days ago by ▴ 10
0
votes
1
reply
141
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No output from read.bismark with bismark cov.files
bsseq methylation
updated 23 days ago by 65k • written 24 days ago by • 0
0
votes
2
replies
276
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Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR CopyhelpeR
24 days ago • updated 19 days ago fer_talavera • 0
0
votes
2
replies
237
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
24 days ago • updated 6 days ago isaac.vock • 0
0
votes
7
replies
347
views
Internet connection for Bioconductor packages in Rstudio in Iran...
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25 days ago • updated 23 days ago needNGS • 0
15
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22
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1.8k
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
26 days ago • updated 5 days ago Chris • 0
3
votes
5
replies
338
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 25 days ago by 50k • written 27 days ago by • 0
45,578 results • Page 3 of 912
Recent ...
Replies
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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