Showing : ChAMP • reset
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Why the order of sample names in the beta matrix affect the analysis results of Champ.DMP? What should I do?
ChAMP limma Bioconductor ChAMPdata
updated 12 months ago by • 0 • written 4.5 years ago by • 0
0
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5
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2.4k
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Loading ChAMP IdatFiles with two different ArrayTypes
ChAMP
updated 4.6 years ago by ▴ 290 • written 4.6 years ago by • 0
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6
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5.0k
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Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
4.6 years ago FWNL15 • 0
1
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1
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2.2k
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How to solve the error in running champ.DMP()
ChAMP
updated 4.8 years ago by ▴ 780 • written 4.8 years ago by ▴ 10
2
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1
reply
1.6k
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How to save results of each step from ChAMP pipeline?
Bioconductor ChAMP
updated 4.8 years ago by ▴ 290 • written 4.8 years ago by ▴ 10
2
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1
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1.9k
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How to download the ChAMP dependency ChAMPdata
ChAMP ChAMPdata
updated 4.8 years ago by 4.3k • written 4.8 years ago by ▴ 10
0
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2
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2.0k
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champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis EPICarray ChAMP Champ.SVD
4.9 years ago arisarkar88 ▴ 40
0
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2
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1.4k
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Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
5.1 years ago sissialva21 • 0
0
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12
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8.5k
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ChAMP input: Beta Matrix?
champ dmr analysis
updated 20 months ago by • 0 • written 10.0 years ago by • 0
0
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0
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827
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ChAMP batch effect
ChAMP
5.2 years ago SMA180043 • 0
1
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2
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1.6k
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what is "sample_well" and "pool_ID" in ChAMP
ChAMP
5.2 years ago Hongbii • 0
2
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7
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4.2k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 2.4 years ago by • 0 • written 5.2 years ago by ▴ 20
3
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5
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3.6k
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation ChAMP
updated 2.0 years ago by • 0 • written 5.2 years ago by • 0
1
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1
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1.4k
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champ.DMP finds different probes in A-vs-B and B-vs-A analysis
DifferentialMethylation ChAMP champ.DMP
updated 5.2 years ago by ▴ 290 • written 5.2 years ago by • 0
1
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3
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4.6k
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normalization combination of noob + BMIQ/Quantile
minfi bmiq noob preprocessQuantile champ
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 50
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1
reply
1.3k
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the function DMR in ChAMP package
ChAMP DMR
updated 5.7 years ago by ▴ 290 • written 5.7 years ago by • 0
0
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1
reply
1.1k
views
rebuild the ChAMP package
ChAMP
updated 5.9 years ago by 25k • written 5.9 years ago by • 0
0
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0
replies
763
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ChAMP DMP col abbreviations stend for what?
ChAMP
5.9 years ago julie • 0
0
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1
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1.1k
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about the ChAMP package, the champ.norm output different results,when run it twice on epic data.
ChAMP
updated 6.0 years ago by ▴ 290 • written 6.0 years ago by • 0
1
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3
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2.2k
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Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
6.1 years ago erwin.tomasich ▴ 10
1
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1
reply
1.3k
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 6.1 years ago by ▴ 90 • written 6.1 years ago by • 0
2
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16
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4.9k
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Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 6.1 years ago by ▴ 290 • written 6.1 years ago by ▴ 20
1
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2
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1.6k
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ChAMP not handling 3+ levels in contrasts
champ
updated 6.4 years ago by ▴ 290 • written 6.4 years ago by • 0
0
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2
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2.0k
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cpg.annotate model requirements
DMRcate ChAMP
updated 6.6 years ago by ▴ 290 • written 6.6 years ago by • 0
0
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1
reply
3.1k
views
Differential Methylation Analysis using ChAMP
ChAMP
updated 5 months ago by 43k • written 6.7 years ago by • 0
2
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4
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2.1k
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bumphunter stalls on "Smoothing coefficients"
bumphunter ChAMP
updated 6.8 years ago by ▴ 290 • written 6.8 years ago by ▴ 10
0
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2
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3.0k
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ChAMP::champ.norm Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x], : task 1 failed - "only defined on a data frame with all…
ChAMP methylation BMIQ
updated 2.3 years ago by • 0 • written 6.8 years ago by ▴ 20
2
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5
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2.7k
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Error in Champ for Bioconductor performing GSEA analysis on Methlayion array data
champ bioconductor methyaltion epic array
updated 7.1 years ago by • 0 • written 7.1 years ago by • 0
1
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8
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3.9k
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Error in Champ for Bioconductor analyzing Methlayion array data
champ bioconductor contrastmatrix compare.group
updated 7.1 years ago by ▴ 290 • written 7.1 years ago by • 0
1
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5
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3.0k
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error while using champ.svd() function
champ
7.2 years ago sinha.puja ▴ 10
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3
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2.2k
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ChAMP Methylation analysis error code "could not find function champ.load"
champ
7.2 years ago sinha.puja ▴ 10
2
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1
reply
1.9k
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 7.3 years ago by ▴ 290 • written 7.3 years ago by ▴ 10
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2
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1.5k
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How can I define which samples are controls and which samples are cases in ChAMP
ChAMP champ.DMP Cases Controls references
7.4 years ago yuabrahamliu • 0
0
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2
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2.3k
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Use ChAMP to Find Differential Methylation Regions (DMR)
ChAMP DMR champ.DMR
7.4 years ago yuabrahamliu • 0
0
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2
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2.7k
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Some terms in EPIC Methylation Analysis
ChAMP SVD Array Slide Sample Plate
updated 7.4 years ago by ▴ 290 • written 7.4 years ago by • 0
0
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2
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3.1k
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ChAMP Normalization on EPIC Methylation Data
ChAMP Normalization FunctionalNormalization methylation EPIC
7.4 years ago yuabrahamliu • 0
0
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4
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1.8k
views
Taking relatedness among individuals into account in differential methylation analysis?
methylation minfi ChAMP
updated 7.5 years ago by ★ 6.5k • written 7.5 years ago by • 0
0
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5
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3.2k
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DNA methylation analysis without raw data IDAT files
r illimina 450k methylation minfi champ tcga
updated 7.5 years ago by ▴ 290 • written 7.5 years ago by ▴ 60
1
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2
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2.0k
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Problem installing ChAMP package.
software error microarray champ methylation
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 10
3
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9
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5.0k
views
champ.runCombat is failing: "invalid 'row.names' length"
champ
7.6 years ago Gurkenkönig ▴ 10
0
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1
reply
1.3k
views
Help with Errors in DMRcate ChAMP package
champ
7.6 years ago urvi • 0
0
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0
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854
views
ChAMP results interpretation
champ
7.7 years ago Giovanni Calice ▴ 160
0
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1
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2.2k
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install ChAMP under Ubuntu 18.04 in R 3.4.4 with error "maximal number of DLLs reached..."
ChAMP software error installation
7.7 years ago chxp • 0
0
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3
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2.1k
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QC and normalization of 450K data from CSVs instead of IDATs
450K CSV normalization minfi ChAMP
updated 7.7 years ago by ▴ 290 • written 7.7 years ago by ▴ 190
0
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3
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1.7k
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Error when running ChAMP package
champ
7.7 years ago hazel.rogers • 0
0
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1
reply
1.9k
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ChAMP functional normalization error "subscript out of bounds"
champ epic microarray normalization minfi
7.8 years ago Laura • 0
1
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3
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1.9k
views
Error biocLite() newest version of ChAMP
R bioclite champ
7.9 years ago rosa_hegi ▴ 10
1
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2
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3.6k
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Beta-matrix - Differential methylation analysis
ChAMP tutorial
7.9 years ago Dave Emir • 0
0
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1
reply
1.2k
views
ChAMP error while lazyloading the latest version ChAMP_2.9.10
ChAMP
updated 7.9 years ago by ▴ 290 • written 7.9 years ago by ▴ 30
2
votes
3
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3.4k
views
"Seems your IDAT file not from one Array"
EPIC methylation ChAMP
updated 7.9 years ago by ▴ 30 • written 7.9 years ago by • 0
156 results • Page 2 of 4
Recent ...
Replies
Answer: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
I'm not familiar with the packages you mention, but the whole reason why Bioconductor has versions is that code and annotation change. Code…
Comment: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa by Gordon Smyth 53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input by Gordon Smyth 53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2 by a2a2hset32aa • 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Votes
Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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