1
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13
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386
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Trying to use enrichGO
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12 days ago • updated 9 days ago fernanda.backsouza ▴ 10
0
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8
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334
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DESeq2 output used for PCA plot on R studio
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7
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1.8k
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6
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397
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How to make boxplot with pairwise and overall p value from Limma
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25 days ago Chris • 0
3
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6
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268
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22 days ago nhaus ▴ 30
0
votes
4
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233
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
16 days ago • updated 13 days ago lonn • 0
0
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3
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109
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Differences in differential analysis methods for RNA-Seq
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updated 1 day ago by ★ 4.1k • written 2 days ago by • 0
1
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3
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854
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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updated 9 days ago by ★ 1.2k • written 14 months ago by ▴ 10
0
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3
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251
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updated 15 days ago by ▴ 850 • written 21 days ago by • 0
0
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2
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239
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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
0
votes
2
replies
294
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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
4 weeks ago • updated 28 days ago fer_talavera • 0
1
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2
replies
151
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Error in champ.load(): The following specified files do not exist
ChAMP
16 days ago • updated 15 days ago Sherin • 0
1
vote
2
replies
209
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significant difference of p-values with dream() after updating VariancePartition
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15 days ago Le • 0
2
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2
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170
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[DiffBind] Obtaining normalization factors
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21 days ago • updated 17 days ago Henry ▴ 10
0
votes
2
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254
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
4 weeks ago • updated 14 days ago isaac.vock • 0
0
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1
reply
510
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Cibersort phenotype file
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updated 24 days ago by • 0 • written 15 months ago by • 0
0
votes
1
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98
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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
0
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1
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130
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Deseq2 Rlog transformation
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updated 18 days ago by ★ 4.1k • written 19 days ago by • 0
0
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1
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174
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DESeq2 gives an error and R crashes
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23 days ago • updated 22 days ago Shefali • 0
0
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1
reply
553
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CopywriteR output
CopywriteR
updated 28 days ago by • 0 • written 2.5 years ago by • 0
0
votes
1
reply
119
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what is the sampleFiles
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updated 17 days ago by 65k • written 17 days ago by • 0
0
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1
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128
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Granges regionCounts not returning the expected number of entries
methylKit
29 days ago • updated 28 days ago Modoc Kesner ▴ 10
0
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1
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338
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Gene names from Matrix
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updated 23 days ago by ▴ 730 • written 7 months ago by • 0
0
votes
1
reply
157
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compareCluster dotplot: how to modify the genesets order
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updated 19 days ago by ★ 3.9k • written 23 days ago by • 0
0
votes
0
replies
62
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
4 days ago Chris • 0
0
votes
0
replies
143
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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
28 days ago andromeda • 0
0
votes
0
replies
96
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One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
8 days ago • updated 18 hours ago glaciya2018 • 0
0
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0
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23
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Handling multiple differential expression comparisons
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0
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0
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85
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queryDGIdb lexical error for some genes
lexicalerror rDGIdb DGIdb json
23 days ago Dennis • 0
0
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0
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94
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Diffbind Error in socketConnection
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18 days ago Virangika • 0
0
votes
0
replies
90
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
21 days ago Stevie Pederson • 0
0
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0
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77
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Unlocking Potential: NURS FPX Strategies and Insights
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12 days ago vaxahey107 • 0
0
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0
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70
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[ChIPseeker] Unable to perform gene ontology analysis
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18 days ago Henry ▴ 10
0
votes
0
replies
92
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I am trying to detect alternative splicing.
ASpli
13 days ago Sebashish • 0
0
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0
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128
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23 days ago Eryn • 0
0
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0
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Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror IsoCorrectoR
17 days ago Maliha Tabassum • 0
0
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0
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22
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dba.plotProfile() plotting and interpretation
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10 hours ago Henry ▴ 10
0
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0
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100
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flowDensity on a flowset
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29 days ago fredrikwallberg • 0
0
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0
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117
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Warning while loading DEP package
DEP
updated 15 days ago by 3.9k • written 15 days ago by • 0
0
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0
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33
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DiffBind: no peaks in DBA object
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1 day ago yvonneh • 0
0
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0
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106
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ggtree tip label position (depth)
ggtree
24 days ago • updated 23 days ago Roope • 0
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0
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26
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1 day ago Ian D. ▴ 70
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0
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29 days ago Macsue • 0
0
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0
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24
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flowStats for CyTOF
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1 day ago tholmes • 0
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0
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77
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9 days ago Dario Strbenac ★ 1.5k
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how to do Differential splicing from SGSeq analysis
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Enzyme Engineering
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16 days ago bocchemistry • 0
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Empty table plot using plotGseaTable()
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2 days ago • updated 6 hours ago Chris • 0
48 results • Page 1 of 1
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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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