User: line.heylen

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line.heylen10
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Posts by line.heylen

<prev • 5 results • page 1 of 1 • next >
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Comment: C: support for EPIC methylation arrays in minfi
... Hi Kasper, I downloaded the new EPIC annotation package at Bioconductor (biocLite("IlluminaHumanMethylationEPICanno.ilm10b2.hg19")) but do not know how to extract the annotation from this data to a dataframe consisting of a column of CpGs with columns like p-values and T statistic; and I getting st ...
written 3.0 years ago by line.heylen10
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Answer: A: support for EPIC methylation arrays in minfi
... Hi Kasper, I downloaded the new EPIC annotation package at Bioconductor (biocLite("IlluminaHumanMethylationEPICanno.ilm10b2.hg19")) but do not know how to extract the annotation from this data to a dataframe consisting of a column of CpGs with columns like p-values and T statistic; and I getting st ...
written 3.0 years ago by line.heylen10
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Comment: C: support for EPIC methylation arrays in minfi
... Dear Kasper, If I already have a list of CpGs with p-values etc, how do I merge this list to the EPIC annotation? For 450K data, I did this by using ChAMP and probe.features, but the EPIC probe.features object entails only chromosome and mapinfo, no information on gene, gene feature (like TSS; exon ...
written 3.2 years ago by line.heylen10
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Comment: C: ChAMP probe.features displays only CHR and MAPINFO, and it entails epic data, wh
... It seems that if I start R again, and load data(probe.features); it successfully loads the 450K annotation. If I load the epic annotation by data(probe.features.epic) probe.features refers then to the epic array and not the 450K array, and includes only the first 2 columns.  ...
written 3.2 years ago by line.heylen10
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ChAMP probe.features displays only CHR and MAPINFO, and it entails epic data, whereas probe.features.epic does not exist
... Hi, I updated R and Bioconductor to use the new ChAMP package for EPIC arrays. In contrast to what is written in the manual, it seems that probe.features.epic does not exist, and that probe.features entails now the EPIC data and not the 450K data. How is this possible?  > dim(probe.features) [ ...
champ written 3.2 years ago by line.heylen10

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