User: c.ryder3

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c.ryder330
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Posts by c.ryder3

<prev • 6 results • page 1 of 1 • next >
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Comment: C: DMRcate results: How to find out which CpG sites constitute each DMR
... Hello. I have updated my question with some more details. ...
written 2.9 years ago by c.ryder330
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DMRcate results: How to find out which CpG sites constitute each DMR
... Hello. The output of DMRcate is the genomic coordinates of regions identified as differentially methylated. DMRcate also tells how many CpG sites are in each DMR. The output looks something like this: coord no.cpgs minfdr Stouffer maxbetafc meanbetafc 39 ...
R bioconductor methylation dmrcate written 2.9 years ago by c.ryder330 • updated 8 months ago by 1234567890
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How to create a design matrix for Cpg.annotate?
... > head(ICGC_2) naive.1 memoryCS.1 naive.2 memoryCS.2 naive.3 memoryCS.3 cg00000029 0.6199970 0.5703951 0.6383819 0.5831206 0.7012571 0.6000816 cg00000108 0.9083578 0.9105157 0.9030611 0.9103147 0.9115842 0.8947593 cg00000109 0.8694214 ...
R bioconductor dmrcate cpg.annotate written 2.9 years ago by c.ryder330 • updated 2.9 years ago by e.rempel890
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A workflow for identification of differentially methylated regions, starting with a data frame of beta values?
... Hello! I have a data frame in R that contains 450K methylation beta values for 6 samples. The probe IDs are the row names and the sample names are the column names. It looks like this: > head(ICGC_2) naive.1 memoryCS.1 naive.2 memoryCS.2 naive.3 memoryCS.3 cg0 ...
450k R bioconductor methylation dmrcate written 2.9 years ago by c.ryder330 • updated 2.9 years ago by halo22150
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Comment: C: How do I map Affymetrix probe IDs to gene symbols in R?
... Thank you! This is really helpful! ...
written 3.1 years ago by c.ryder330
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How do I map Affymetrix probe IDs to gene symbols in R?
... I have an ExpressionSet, combArr.eset, that contains Affymetrix Human Genome U133 Plus 2.0 Array gene expression data. I also have a matrix, exprs_combArr.eset, that contains the expression data for combArr.eset. The row names for exprs_combArr.eset are the hgu133plus2 probe IDs, and the column name ...
R bioconductor written 3.1 years ago by c.ryder330 • updated 3.1 years ago by russhh5.4k

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