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0
votes
0
answers
7
views
0
answers
why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM_tumor_mean/FPKM_normal_mean)?
edger deseq2 counts fpkm fc written 1 hour ago by ZihaoXing • 0
0
votes
1
answer
31
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1
answer
use only lib size as normalizing factor in edgeR
edger written 20 hours ago by Udi Landau • 20 • updated 9 hours ago by Aaron Lun • 21k
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votes
0
answers
23
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0
answers
how to calculate heterogeneity for meta-analysis of p-value
pvalue meta analysis written 22 hours ago by ningq669 • 0
2
votes
2
answers
233
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2
answers
Opencyto - detector name not found in flow data, but pretty sure it's there
flowcore opencyto flow cytometry written 11 months ago by Andrew Box • 10 • updated 1 day ago by Jiang, Mike • 1.2k
2
votes
1
answer
48
views
1
answer
FlowJo workspace cannot be parsed with flowworkspace
flowworkspace parseworkspace written 1 day ago by vonskopnik • 10 • updated 1 day ago by Jiang, Mike • 1.2k
1
vote
2
answers
73
views
2
answers
ChIPQC: error during annotation compilation
chipqc written 5 days ago by hdingwall • 10 • updated 1 day ago by Thomas Carroll • 400
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votes
0
answers
34
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0
answers
Error in print.header("GDCquery: Searching in GDC database", "section") :could not find function "print.header",
dplyr tcgabiolinks dt written 1 day ago by Mithil Gaikwad • 0
0
votes
1
answer
40
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1
answer
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 interactions contrast rna-seq written 1 day ago by Maithê Barros • 0 • updated 1 day ago by Michael Love ♦ 19k
0
votes
1
answer
71
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1
answer
DESingle, Differential expression in single cell rna seq (scRNA)
desingle different expression status written 16 days ago by bioinfo.himanshu • 0 • updated 1 day ago by miaoz13 • 0
0
votes
1
answer
32
views
1
answer
Unable to build GDS with more than 255 scaffolds?
gwas gds genesis written 2 days ago by naglemi • 0 • updated 2 days ago by zhengx • 20
0
votes
1
answer
31
views
1
answer
Error in data.frame for limmaCtData function
limma software error data.frame written 3 days ago by azmir004 • 0 • updated 2 days ago by Gordon Smyth ♦ 35k
0
votes
1
answer
86
views
1
answer
DESEQ2 / Phyloseq contrasts no longer work as before following update
phyloseq deseq2 written 3 days ago by eoin • 0
0
votes
0
answers
43
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0
answers
DiffBind confuses coordinates of peaks
diffbind atacseq written 2 days ago by gtechbio • 0
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0
answers
32
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0
answers
Report error in the stage of "Prepare the 'metadata' data frame" when running exomepeak() or metdiff with
exomepeak written 2 days ago by 939930094 • 0
1
vote
1
answer
68
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1
answer
DESeq2 design nested or time course
deseq2 nested design written 2 days ago by katarina.truve • 0 • updated 2 days ago by Michael Love ♦ 19k
2
votes
1
answer
74
views
1
answer
Deseq: What does "BaseMean" mean?
deseq2 written 3 days ago by 183227851 • 0 • updated 3 days ago by Guido Hooiveld • 2.3k
1
vote
1
answer
74
views
1
answer
How to filter overlaping EBImage objects?
ebimage written 15 days ago by atbest09 • 0 • updated 3 days ago by Wolfgang Huber ♦ 13k
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0
answers
23
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0
answers
Changing vertical scale to linear for expression reporting of DESeqDataSet
reportingtools deseq2 written 3 days ago by trebbiano • 0
6
votes
2
answers
61
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2
answers
Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
limma rna-seq repeated measures mixed model written 3 days ago by mikhael.manurung • 0 • updated 3 days ago by Gordon Smyth ♦ 35k
2
votes
1
answer
87
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1
answer
Correct formulation of contrasts of interest regarding an RNA-Seq gene expression analysis with edgeR
rnaseq edger design and contrast matrix multifactorial design written 5 days ago by fotakisg • 0 • updated 3 days ago by Aaron Lun • 21k
0
votes
0
answers
32
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0
answers
some errors in cytofWorkflow2 description
cytofworkflow written 5 days ago by o.hunewald • 0 • updated 3 days ago by James W. MacDonald ♦ 47k
0
votes
1
answer
31
views
1
answer
Issue using ballgown
genomeinfodb software error ballgown genomeinfodbdata written 4 days ago by dualeahmed • 0 • updated 3 days ago by James W. MacDonald ♦ 47k
0
votes
1
answer
47
views
1
answer
Including batch effects in the differential expression of gene analysis
ballgown new tuxedo pipleine written 3 days ago by amy16 • 0 • updated 3 days ago by James W. MacDonald ♦ 47k
0
votes
1
answer
35
views
1
answer
CopywriteR - low coverage-regions display very low numbers
copynumber copywriter written 3 days ago by magdaaverte • 0 • updated 3 days ago by t.kuilman ♦ 140
1
vote
1
answer
36
views
1
answer
Minfi read.metharray.sheet error
dataimport minfi minfidata methylation missmethyl written 4 days ago by moldach • 10 • updated 3 days ago by James W. MacDonald ♦ 47k
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