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Answer: Answer: limma Intercept vs No-intercept models completely changing DMR results?
2 days ago James W. MacDonald 65k
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158
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Answer: Answer: Too many significant genes when integrating gtex and tcga
2 days ago James W. MacDonald 65k
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197
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Answer: Answer: Once again a "Model matrix not full rank"
3 days ago James W. MacDonald 65k
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96
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Answer: Answer: DESeq2 v1.35.0
3 days ago James W. MacDonald 65k
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153
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Answer: Answer: Store output of matchPWM()
4 days ago James W. MacDonald 65k
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221
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Answer: Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
4 days ago James W. MacDonald 65k
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225
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Answer: Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
5 days ago James W. MacDonald 65k
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201
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Answer: Answer: Help with error using camera() in limma
5 days ago James W. MacDonald 65k
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238
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Answer: Answer: Assist me in determining whether the analysis process using the limma package ha
6 days ago James W. MacDonald 65k
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326
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Answer: Answer: Math expression in shapeCustom legend in EnhancedVolcano
10 days ago James W. MacDonald 65k
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1
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389
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Answer: Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
10 days ago James W. MacDonald 65k
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262
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Answer: Answer: get BM error
11 days ago James W. MacDonald 65k
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240
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Answer: Answer: How to retrieve gene ontology GO class from gene list?
11 days ago James W. MacDonald 65k
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235
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Answer: Answer: Error EPICv2 ChAMP
13 days ago James W. MacDonald 65k
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126
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Answer: Answer: FDR via q-value
13 days ago James W. MacDonald 65k
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302
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Answer: Answer: Error for AnnotationForge makeOrgPackageFromNCBI function
13 days ago James W. MacDonald 65k
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154
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Answer: Answer: Error retrieving ensembl gene id using biomaRt...
16 days ago James W. MacDonald 65k
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190
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Answer: Answer: OrgDb for maize
16 days ago James W. MacDonald 65k
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139
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Answer: Answer: SNP locus package for mouse?
19 days ago James W. MacDonald 65k
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194
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Answer: Answer: flowStats Search Error
19 days ago James W. MacDonald 65k
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2
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947
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Answer: Answer: Convert Seurat Object to Summarised Experiment or ExpressionSet
25 days ago James W. MacDonald 65k
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351
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Answer: Answer: Why is my gene not significantly differentially expressed?
25 days ago James W. MacDonald 65k
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426
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Answer: Answer: Not fully paired differential gene expression analysis
26 days ago James W. MacDonald 65k
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151
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Answer: Answer: BAM write error in HTSeqGenie
26 days ago James W. MacDonald 65k
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494
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Answer: Answer: GSVA on separate healthy and disease datasets
26 days ago James W. MacDonald 65k
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336
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Answer: Answer: permutation test in edgeR
27 days ago James W. MacDonald 65k
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180
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Answer: Answer: How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
27 days ago James W. MacDonald 65k
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262
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Answer: Answer: Lib sizes in the DGE object are different from original lib sizes
4 weeks ago James W. MacDonald 65k
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233
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Answer: Answer: MethylKit read issue
4 weeks ago James W. MacDonald 65k
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313
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Answer: Answer: Help with design.matrix
4 weeks ago James W. MacDonald 65k
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171
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Answer: Answer: What to the log 2 fold changes mean using LRT on time course in DESeq2
4 weeks ago James W. MacDonald 65k
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167
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Answer: Answer: DESeq2 - Missing values in count matrix
4 weeks ago James W. MacDonald 65k
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433
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Answer: Answer: DESeq2 step-by-step Normalization then DGE separately & Normalization methods an
4 weeks ago James W. MacDonald 65k
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190
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Answer: Answer: voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
4 weeks ago James W. MacDonald 65k
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337
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Answer: Answer: unable to access Annotationhub latest record
4 weeks ago James W. MacDonald 65k
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173
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Answer: Answer: pca with VST of DESeq2 give 100% variance in PC1
4 weeks ago James W. MacDonald 65k
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145
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Answer: Answer: Multiple affymatrix IDs mapping to a single gene name
4 weeks ago James W. MacDonald 65k
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110
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Answer: Answer: Brachypodium distachyon db
4 weeks ago James W. MacDonald 65k
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183
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Answer: Answer: How to make GSEAplot with chip set
4 weeks ago James W. MacDonald 65k
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180
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Answer: Answer: Gene Ontology doubt
4 weeks ago James W. MacDonald 65k
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2
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245
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Answer: Answer: Minfi - estimatecellscount
5 weeks ago James W. MacDonald 65k
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229
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Answer: Answer: WGCNA: analysis of complex trait associations with regressions
5 weeks ago James W. MacDonald 65k
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138
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Answer: Answer: Trimming a section of a scaffold from a genome
5 weeks ago James W. MacDonald 65k
1
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2
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535
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Answer: Answer: Microarray Limma Model fitting and DEG
5 weeks ago James W. MacDonald 65k
1
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230
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Answer: Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
5 weeks ago James W. MacDonald 65k
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176
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Answer: Answer: bioconductor emailing list
5 weeks ago James W. MacDonald 65k
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217
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Answer: Answer: How to extract counts from a DESeq dataset ordered by a specific sample?
5 weeks ago James W. MacDonald 65k
2
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458
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Answer: Answer: Batch Effect Correction, Gene Filtering
6 weeks ago James W. MacDonald 65k
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214
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Answer: Answer: Non-empty droplets versus good quality cells
6 weeks ago James W. MacDonald 65k
4
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233
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Answer: Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
6 weeks ago James W. MacDonald 65k
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