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DNAMethylation
•
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0
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7
replies
239
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Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
7 days ago • updated 1 day ago
hortense96
• 0
0
votes
0
replies
78
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
20 days ago
Macsue
• 0
0
votes
6
replies
306
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 14 days ago by
Tim Peters
▴ 170 • written 22 days ago by
s.malik
• 0
0
votes
1
reply
235
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation
GO
MethylationArray
missMethyl
EPICv2
updated 7 weeks ago by
belinda.phipson
▴ 40 • written 7 weeks ago by
s.malik
• 0
0
votes
4
replies
379
views
Seeking Strategies for Managing Duplicate CpG Entries in EPIC v2 Manifest
DNAMethylation
EPICv2
IlluminaHumanMethylationEPICmanifest
updated 9 weeks ago by
James W. MacDonald
65k • written 9 weeks ago by
rae.alshammari
▴ 10
1
vote
4
replies
377
views
limma design model for categorical variable
DNAMethylation
limmaGUI
biostatistics
limma
updated 10 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Jitendra
▴ 10
0
votes
1
reply
169
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
updated 5 weeks ago by
Simon Pearce
• 0 • written 11 weeks ago by
User3088
• 0
1
vote
4
replies
438
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation
MethylationArray
methylationArrayAnalysis
illumina
11 weeks ago
mikat
• 0
0
votes
1
reply
484
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation
missMethyl
Pathways
12 months ago
Grace
• 0
2
votes
6
replies
1.0k
views
cpg.annotate() in DMRcate error
DNAMethylation
methylationArrayAnalysis
DMRcate
MethylationArrayData
MethylationArray
updated 12 months ago by
Tim Peters
▴ 170 • written 12 months ago by
Grace
• 0
2
votes
6
replies
929
views
No enriched GO terms CpGs
DNAMethylation
missMethyl
updated 13 months ago by
belinda.phipson
▴ 40 • written 13 months ago by
Joana
• 0
0
votes
0
replies
531
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation
wateRmelon
Computation
minfi
20 months ago
calen.p.ryan
• 0
3
votes
8
replies
1.4k
views
Annotation using QSEA package
DNAMethylation
QSEA
MEDIP
2.8 years ago
rtrivedi1
▴ 10
3
votes
5
replies
2.1k
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation
ChAMP
updated 8 weeks ago by
sup0903
• 0 • written 3.4 years ago by
Hongbii
• 0
14 results • Page
1 of 1
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Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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