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updated 9 days ago by 41k • written 9 days ago by ▴ 20
1
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4
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309
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9 days ago • updated 7 days ago winwater0928 • 0
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 9 days ago by 41k • written 10 days ago by ▴ 40
1
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1
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166
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Citation for edgeR user guide
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106
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333
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0
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0
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199
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minfi::read.metharray.exp
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0
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2
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238
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featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
10 days ago • updated 8 days ago shuwangxinze1996 • 0
1
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2
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990
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DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
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updated 10 days ago by ▴ 180 • written 14 months ago by ▴ 10
0
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2
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151
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3
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3
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219
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updated 10 days ago by 41k • written 11 days ago by • 0
1
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4
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223
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updated 11 days ago by 65k • written 15 days ago by • 0
0
votes
1
reply
122
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FDR via q-value
qvalue
updated 11 days ago by 65k • written 14 days ago by • 0
0
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5
replies
289
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Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 9 days ago by 65k • written 12 days ago by • 0
0
votes
2
replies
202
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RNAseq:Technical replicates from different batches
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14 days ago • updated 11 days ago catv • 0
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3
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1.2k
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6
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12
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BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
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6 months ago • updated 11 days ago shepherl 3.9k
1
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13
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385
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Trying to use enrichGO
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12 days ago • updated 9 days ago fernanda.backsouza ▴ 10
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0
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77
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12 days ago vaxahey107 • 0
14
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17
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Why p value inconsistent when using different number of pathway score?
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13 days ago • updated 2 days ago Chris • 0
0
votes
0
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92
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I am trying to detect alternative splicing.
ASpli
13 days ago Sebashish • 0
3
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3
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Error retrieving ensembl gene id using biomaRt...
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2
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183
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OrgDb for maize
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1
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6
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edgeR
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3
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3
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Log-cpm values from limma
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FGSEA pre-ranked input in increasing order or decreasing
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15 days ago sropri • 0
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150
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Adding columns to DEXSeqResults object
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117
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Warning while loading DEP package
DEP
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132
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rlog transformation
DESeq2
updated 15 days ago by 41k • written 15 days ago by • 0
0
votes
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reply
109
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
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16 days ago • updated 7 days ago ussarizona ▴ 10
0
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130
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covariate with negative and positive values
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updated 15 days ago by 41k • written 17 days ago by • 0
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DESEQ2 output gives multiple groups when only 2 groups are present
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significant difference of p-values with dream() after updating VariancePartition
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15 days ago Le • 0
1
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ChAMP
16 days ago • updated 15 days ago Sherin • 0
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Input Question for deseq.r
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updated 15 days ago by ★ 4.1k • written 16 days ago by • 0
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4
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Differential peaks that were not identified in diffbind were identified in diseq2
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Methylation Analysis experiment design using Limma
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17 days ago Maliha Tabassum • 0
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updated 17 days ago by 3.9k • written 18 days ago by • 0
203 results • Page 2 of 5
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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