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Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
11 days ago
Felix
• 0
0
votes
1
reply
238
views
Error in reading my csv file in minfi
minfiDataEPIC
minfi
updated 3 months ago by
Basti
▴ 750 • written 3 months ago by
Ana
• 0
0
votes
1
reply
385
views
Create design matrix for differential methylation analysis
Annotation
annotate
DifferentialMethylation
minfiDataEPIC
updated 5 months ago by
Basti
▴ 750 • written 5 months ago by
titangerd
• 0
0
votes
6
replies
1.3k
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annotation EpicV2
minfiDataEPIC
EpicV2
updated 6 months ago by
Zuguang Gu
▴ 240 • written 7 months ago by
Izabela.ams
• 0
0
votes
1
reply
338
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC
minfi
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
phelankj
• 0
0
votes
1
reply
2.2k
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Warning messages in detecting P-values
minfiDataEPIC
methylationArrayAnalysis
updated 7 months ago by
ATpoint
★ 3.9k • written 7 months ago by
rae.alshammari
▴ 10
0
votes
1
reply
485
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis
minfi
MethylationArrayData
minfiDataEPIC
MethylationArray
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
Grace
• 0
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Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
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Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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