Showing : methylation • reset
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TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
6.9 years ago gerald.mccollam • 0
4
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4
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2.0k
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Illumina Methylation 27k minfi
microarray methylation illumina27k minfi
updated 7.0 years ago by ★ 6.5k • written 7.0 years ago by • 0
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0
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1.7k
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Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
7.1 years ago • updated 7.0 years ago moldach ▴ 20
0
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1
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1.4k
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Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
1
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2
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2.0k
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Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 7.2 years ago by ★ 1.4k • written 7.2 years ago by • 0
2
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1
reply
2.0k
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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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0
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1.2k
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All fragments/sequences captured using MeDIP are methylated?
medip-seq methylation CpGs
7.3 years ago saripalligautam86 ▴ 10
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
1
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2
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2.5k
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Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 7.5 years ago by 68k • written 7.5 years ago by ▴ 20
2
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8
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2.9k
views
edgeR: design matrix for methylation analysis
edger methylation
updated 7.5 years ago by 53k • written 7.7 years ago by • 0
0
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0
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1.1k
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Error while using TCGAanalyze_DMR for >2 groups
methylation tcgabiolinks R gleason score TCGAanalyze_DMR
7.5 years ago mtkk94 • 0
5
votes
9
replies
2.6k
views
limma Multi-level Experiments correcting for continuous covariates
limma epic methylation limma design matrix covariates
updated 7.5 years ago by ★ 29k • written 7.5 years ago by • 0
0
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4
replies
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
1
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2
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2.0k
views
Problem installing ChAMP package.
software error microarray champ methylation
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 10
0
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3
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2.2k
views
Minfi error when using force=TRUE in read.metharray
minfi methylation epic
7.6 years ago jbar3141 • 0
1
vote
1
reply
3.7k
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 7.6 years ago by ▴ 20 • written 7.6 years ago by • 0
0
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0
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1.7k
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Interpretation of control strip and beta density plots for Illumina methylation array data using minFi
minfi methylation EPIC
7.6 years ago sichan • 0
0
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2
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1.9k
views
MethylKit DSS Package
R bioconductor methylation methylkit
updated 7.6 years ago by ▴ 20 • written 7.6 years ago by • 0
0
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0
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1.6k
views
Job: Post-doc in Prostate Cancer Research (Statistics / Computational Biology) at University of St Andrews (+PhD position also available)
cancer sequencing rnaseq methylation smallrna Job
7.7 years ago Andy Lynch ▴ 120
1
vote
1
reply
2.5k
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names methylation illumina convertids
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 10
0
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0
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1.3k
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which value from ruvadj in missMethyl can present methylation status
methylation missmethyl RUV batch effect
7.8 years ago RC • 0
0
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0
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1.7k
views
DSS DMLTest Prior Estimate of theta dispersion
DSS dmltest bayesian statistics methylation
7.9 years ago floriandeckert ▴ 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
0
votes
6
replies
2.4k
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq methylation ensembl ucsc limma
8.0 years ago dusan.petrovic • 0
2
votes
2
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2.2k
views
dmrseq: cannot adjust for a covariate
dmrseq dmr dmrs bisulfite methylation
updated 8.0 years ago by ▴ 60 • written 8.1 years ago by • 0
0
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0
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1.5k
views
differential methylation analysis with RnBeads
rnbeads methylation methylationepic dna methylation
8.0 years ago gabrielrfries • 0
0
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2
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2.6k
views
Error code using ChAMP/Bioconductor, unable to load data from EPIC methylation array
bioconductor methylation epic microarray champ
8.1 years ago csappleby-mallinder1 • 0
0
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2
replies
1.4k
views
methylPipe: how BSprepare handles zeros
methylation methylPipe
updated 8.3 years ago by ▴ 200 • written 8.3 years ago by • 0
0
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13
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3.6k
views
handling missing data (NA) for methylaion analysis in Limma
limma missing data methylation normalization
updated 8.4 years ago by ★ 29k • written 8.4 years ago by ▴ 10
0
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0
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1.1k
views
About the meaning of the value column in minfi package
minfi methylation
8.6 years ago Antonio M. • 0
1
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3
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2.0k
views
Minfi returning incorrect beta values
minfi illumina illumina450k methylation R
8.6 years ago ezrabekele17 • 0
3
votes
1
reply
1.9k
views
Limma Model Design
limma methylation microarray
updated 8.7 years ago by ★ 29k • written 8.7 years ago by • 0
1
vote
2
replies
2.3k
views
DMRcate results file ordered by genomic location and not Stouffer p-val?
DMRcate dmrcate methylation
updated 8.8 years ago by ▴ 230 • written 8.8 years ago by • 0
0
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0
replies
1.3k
views
minfi error with dmpfinder
methylation illumina
8.8 years ago indranipoddar • 0
0
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1
reply
2.4k
views
How to convert GenomicRatioSet to RGChannelSet in minfi::compartments()
minfi estimateCellCounts methylation
updated 8.8 years ago by ★ 6.5k • written 8.8 years ago by ▴ 10
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0
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1.0k
views
Is there any way to parallelise sva functions?
sva methylation
8.8 years ago stewart999 ▴ 10
0
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6
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4.4k
views
difference in detection p-values from Minfi vs. GenomeStudio
minfi genomestudio methylation
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 40
0
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7
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4.2k
views
Is anyone able to explain the statistics behind the dmpFinder function in minfi package?
minfi methylation dmpfinder limma
updated 8.8 years ago by • 0 • written 9.5 years ago by ▴ 20
0
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2
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3.3k
views
Illumina methylationEPIC demo data in IDAT format?
methylation illumina EPIC methylationepic idat
updated 8.8 years ago by ★ 4.1k • written 8.8 years ago by • 0
0
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2
replies
2.1k
views
should i include PCs or MDSs as covariates in methylation study?
limma methylation R covariate MDS
updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
1
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3
replies
2.2k
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 8.9 years ago by 68k • written 8.9 years ago by ▴ 10
0
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1
reply
2.4k
views
Epigenetic clock (Horvath): package?
methylation illimina 450k methylation epigenetics minfi
updated 9.0 years ago by ▴ 60 • written 9.1 years ago by ▴ 120
0
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1
reply
1.7k
views
champ.load getting filtered RGChannelSet
champ methylation
updated 9.0 years ago by ▴ 90 • written 9.1 years ago by ▴ 20
0
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4
replies
2.3k
views
minfi "mapToGenome" dimension error
methylation epic microarray minfi methylationepic
9.0 years ago nhejazi • 0
0
votes
5
replies
3.1k
views
Different errors when attempting to normalize using wateRmelon (v1.1.18)
wateRmelon methylation EPIC normalization
9.1 years ago Wade Davis ▴ 60
4
votes
4
replies
3.9k
views
bumphunter output clarification: p values achieved with b=1000: further correction needed?
methylation dmr analysis bumphunter
updated 9.2 years ago by 68k • written 9.2 years ago by • 0
0
votes
3
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1.9k
views
BiSeq. Model beta regression on resampled data.
biseq methylation dmr analysis
updated 9.2 years ago by ▴ 130 • written 9.2 years ago by • 0
0
votes
0
replies
1.5k
views
Bach effect and PEER/RUV correction on large population
methylation gene expression sva batch effect ruv
9.2 years ago carleshf • 0
0
votes
0
replies
1.1k
views
nPCs in minfi's Functional Normalization
minfi normalization methylation
9.2 years ago carlos.ruiz • 0
1
vote
4
replies
2.0k
views
M3D package in Bioconductor 3.4
bioconductor methylation
updated 9.2 years ago by ▴ 80 • written 9.3 years ago by • 0
142 results • Page 2 of 3
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Answer: GSEA error by James W. MacDonald 68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Answer: Unable to find ENTREZ IDs by James W. MacDonald 68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
Answer: Inconsistencies between accessor functions for TxDb databases with selected seql by a2a2hd42aa • 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
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Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
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