User: Line Heylen

gravatar for Line Heylen
Line Heylen10
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Location:
Belgium
Last seen:
2 years, 6 months ago
Joined:
3 years, 10 months ago
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l**********@gmail.com

Posts by Line Heylen

<prev • 7 results • page 1 of 1 • next >
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Answer: A: ChAMP probe.features displays only CHR and MAPINFO, and it entails epic data, wh
... The solution offered by Tian Yuang: load data(illuminaEPICGr), which contains the information. When you load the data illuminaEPICGr, the variable in R will be named as "illumina450GR", but it's actually the EPIC array's annotation. ...
written 2.9 years ago by Line Heylen10
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Answer: A: ChAMP probe.features displays only CHR and MAPINFO, and it entails epic data, wh
... I did, this does not seem to be the problem. When I restart R; load Champ and enter data(probe.features); it successfully loads the 450K annotation with all columns. If I then load the epic annotation by data(probe.features.epic) probe.features refers to the epic array and not the 450K array and inc ...
written 3.0 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 ...
epic dna methylation champ annotation written 3.0 years ago by Line Heylen10
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error with gene selection in CMA package in R
... Hi, I would like to use the CMA package to find a classifier among gene expression data from 2 groups.  I have a normalized and filtered microarray gene expression data file, and a vector containing the sample group information. I am able to generate learning sets (by fiveCVdat <- GenerateLearn ...
R microarray cma written 3.7 years ago by Line Heylen10
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how to find differentially methylated regions (for example with probe lasso in Champ) based on regression continuous variable ~ beta (with CpGassoc)
... Hi, I performed 450K Illumina methylation chips on human samples, and want to search for the association between a continuous variable and beta, adjusted for other covariates. For this, I used the CpGassoc package in R. I would also like to search for differentially methylated regions based on the ...
R written 3.7 years ago by Line Heylen10
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different color for highlighting genes in Manhattan plot in qqman
... Hi, I'm using qqman in R to draw a Manhattan plot (not SNPs, but DNA methylation data of 450K Illumina arrays, but this won't make a difference for this particular question).  I can highlight specific CpGs of interest using the highlight = in the manhattan function, however, I would like to change ...
genome R written 3.7 years ago by Line Heylen10
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How to use normalized expression values as input for limma?
... Hi!     I'm a beginner in microarray analysis. I have an excel file with RMA normalized expression values: with probe IDs as rows and my RNA samples as columns. I can use this for GSEA, etc.. , but it seems that for analysis with limma in R, I would need the raw files and normalize them with affy ...
R written 3.8 years ago by Line Heylen10 • updated 3.8 years ago by Irsan6.8k

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