Showing : ChAMP • reset
0
votes
3
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157
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methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19 ChAMP minfi
7 weeks ago • updated 4 days ago ramonfallon • 0
0
votes
1
reply
49
views
champ.SVD() error, assumes standard class() function will return single string
ChAMP
updated 4 days ago by ▴ 280 • written 4 days ago by • 0
0
votes
4
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184
views
ERROR happens when install "DSS" package
methylationArrayAnalysis ChAMP DMP DSS
9 days ago • updated 8 days ago 16301050225 • 0
0
votes
4
replies
145
views
Problem installing ChAMP package.
ChAMP
4 weeks ago Yu-min • 0
0
votes
1
reply
93
views
How to control for confounders in champ.DMP and champ.DMR?
ChAMP
updated 6 weeks ago by ▴ 280 • written 6 weeks ago by • 0
0
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1
reply
138
views
Error in ChAMP GUI
ChAMP shiny ChAMPdata
updated 9 weeks ago by • 0 • written 10 weeks ago by • 0
0
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1
reply
291
views
Error using ChAMP SVD analysis
ChAMP
updated 4 months ago by • 0 • written 10 months ago by • 0
0
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0
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161
views
Error in champ.svd - function 'EstDimRMTv2' within champ.svd acting inconsistently?
minfiData ChAMP
4 months ago behr201 • 0
0
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3
replies
309
views
Wrong terminology used on champ.load() output of ChAMP package?
ChAMPdata ChAMP
updated 5 months ago by ▴ 280 • written 5 months ago by • 0
0
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0
replies
223
views
Problem loading Red channel idat files with champ.load
R MethylationArrayData ChAMP
5 months ago Paulina • 0
0
votes
3
replies
2.1k
views
Problem loading R packages on MacBook Pro
newpackage ChAMP
updated 4 weeks ago by • 0 • written 6 months ago by • 0
0
votes
2
replies
203
views
problems opening ChAMP
ChAMP
updated 6 months ago by ▴ 280 • written 6 months ago by • 0
0
votes
1
reply
245
views
error in champ.norm
champ.norm ChAMP
updated 7 months ago by 3.5k • written 7 months ago by • 0
0
votes
0
replies
197
views
ChAMP.CNA analysis
CopyNumberPlots ChAMP CopyNumberVariation CopyNumberVariationData
8 months ago FWNL15 • 0
0
votes
2
replies
364
views
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
9 months ago • updated 8 months ago Jinyue • 0
0
votes
5
replies
373
views
Loading ChAMP IdatFiles with two different ArrayTypes
ChAMP
updated 9 months ago by ▴ 250 • written 10 months ago by • 0
0
votes
6
replies
851
views
Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
10 months ago FWNL15 • 0
1
vote
1
reply
263
views
How to solve the error in running champ.DMP()
ChAMP
updated 12 months ago by ▴ 280 • written 12 months ago by ▴ 10
2
votes
1
reply
276
views
How to save results of each step from ChAMP pipeline?
Bioconductor ChAMP
updated 12 months ago by ▴ 250 • written 12 months ago by ▴ 10
2
votes
1
reply
312
views
How to download the ChAMP dependency ChAMPdata
ChAMP ChAMPdata
updated 12 months ago by 3.1k • written 12 months ago by ▴ 10
0
votes
2
replies
397
views
champ.SVD() : Error in while (step == 0) { : missing value where TRUE/FALSE needed
methylationArrayAnalysis EPICarray ChAMP Champ.SVD
13 months ago arisarkar88 • 0
0
votes
1
reply
328
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 15 months ago by ▴ 280 • written 15 months ago by • 0
0
votes
2
replies
379
views
Error myDMP not found
Illumina methylationArrayAnalysis ChAMPdata ChAMP
15 months ago sissialva21 • 0
0
votes
11
replies
3.8k
views
ChAMP input: Beta Matrix?
champ dmr analysis
updated 16 months ago by • 0 • written 6.2 years ago by • 0
0
votes
0
replies
216
views
ChAMP batch effect
ChAMP
17 months ago SMA180043 • 0
1
vote
2
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422
views
what is "sample_well" and "pool_ID" in ChAMP
ChAMP
17 months ago Hongbii • 0
1
vote
6
replies
990
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 6 weeks ago by • 0 • written 17 months ago by ▴ 10
3
votes
4
replies
668
views
Why the LogFC and delta-beta value are different in ChAMP
DNAMethylation ChAMP
17 months ago Hongbii • 0
1
vote
1
reply
260
views
champ.DMP finds different probes in A-vs-B and B-vs-A analysis
DifferentialMethylation ChAMP champ.DMP
updated 18 months ago by ▴ 250 • written 18 months ago by • 0
1
vote
3
replies
977
views
normalization combination of noob + BMIQ/Quantile
minfi bmiq noob preprocessQuantile champ
updated 20 months ago by 59k • written 20 months ago by ▴ 50
0
votes
1
reply
259
views
the function DMR in ChAMP package
ChAMP DMR
updated 23 months ago by ▴ 250 • written 23 months ago by • 0
0
votes
6
replies
551
views
error with champ.load
ChAMP champ methylation
updated 9 months ago by • 0 • written 2.1 years ago by • 0
0
votes
1
reply
212
views
rebuild the ChAMP package
ChAMP
updated 2.1 years ago by 25k • written 2.1 years ago by • 0
0
votes
0
replies
178
views
ChAMP DMP col abbreviations stend for what?
ChAMP
2.1 years ago julie • 0
0
votes
1
reply
365
views
about the ChAMP package, the champ.norm output different results,when run it twice on epic data.
ChAMP
updated 2.2 years ago by ▴ 250 • written 2.2 years ago by • 0
1
vote
3
replies
497
views
Skewed beta-distribution from Methylation EPIC array data
ChAMP EPIC Illumina Methylation
2.3 years ago erwin.tomasich ▴ 10
1
vote
1
reply
306
views
Issue with ChAMP DMP.GUI
ChAMP champ methylation EPIC
updated 2.3 years ago by ▴ 90 • written 2.3 years ago by • 0
2
votes
16
replies
1.0k
views
Methylation EPIC array: ChAMP package-champ.load added probes?
methylation epic champ champ.load() Methylation array
updated 2.4 years ago by ▴ 250 • written 2.4 years ago by ▴ 10
1
vote
2
replies
437
views
ChAMP not handling 3+ levels in contrasts
champ
updated 2.6 years ago by ▴ 250 • written 2.7 years ago by • 0
0
votes
2
replies
500
views
cpg.annotate model requirements
DMRcate ChAMP
updated 2.8 years ago by ▴ 250 • written 2.8 years ago by • 0
0
votes
1
reply
949
views
Tutorial: Differential Methylation Analysis using ChAMP
champ Tutorial
updated 2.9 years ago by ▴ 250 • written 2.9 years ago by • 0
2
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4
replies
654
views
bumphunter stalls on "Smoothing coefficients"
bumphunter ChAMP
updated 3.0 years ago by ▴ 250 • written 3.0 years ago by ▴ 10
0
votes
1
reply
750
views
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 3.0 years ago by ▴ 250 • written 3.0 years ago by ▴ 20
2
votes
5
replies
1.1k
views
Error in Champ for Bioconductor performing GSEA analysis on Methlayion array data
champ bioconductor methyaltion epic array
updated 3.3 years ago by • 0 • written 3.3 years ago by • 0
1
vote
8
replies
1.4k
views
Error in Champ for Bioconductor analyzing Methlayion array data
champ bioconductor contrastmatrix compare.group
updated 3.4 years ago by ▴ 250 • written 3.4 years ago by • 0
1
vote
5
replies
1.1k
views
error while using champ.svd() function
champ
3.4 years ago sinha.puja ▴ 10
0
votes
3
replies
804
views
ChAMP Methylation analysis error code "could not find function champ.load"
champ
3.4 years ago sinha.puja ▴ 10
2
votes
1
reply
672
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 3.5 years ago by ▴ 250 • written 3.5 years ago by • 0
0
votes
2
replies
502
views
How can I define which samples are controls and which samples are cases in ChAMP
ChAMP champ.DMP Cases Controls references
3.6 years ago yuabrahamliu • 0
0
votes
2
replies
838
views
Use ChAMP to Find Differential Methylation Regions (DMR)
ChAMP DMR champ.DMR
3.6 years ago yuabrahamliu • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
Ok.. thanks for your valuable suggestion and quick replies. I have generated an MA plot using plotMASwish. thanks ekta
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by Michael Love 37k
Sorry, I haven't seen this. Maybe try filtering low count genes? ``` keep <- rowSums(counts(dds) >= 10) >= X dds <- dds[keep,] # then run …
Comment: Transcript-level differential expression using DESeq2 by Michael Love 37k
To show some extent of the DTE you can plot the LFC of the significant set and their mean count, we have `plotMASwish` to do this. Another…
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
No, the Volcano plot is not essential. I just wanted to show DETs with the help of a plot. Could you suggest a way for it? What are the oth…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Hi Michael, I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
Votes
Comment: Transcript-level differential expression using DESeq2
Comment: Transcript-level differential expression using DESeq2
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
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