User: fortin946

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fortin946180
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Posts by fortin946

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Comment: C: How to apply preprocessing methods from minfi package on an output file from Gen
... You are correct, the control probes are lost with the Genome Studio preprocessing and are needed for the functional normalization algorithm; I believe there is a way to get those probes from the Genome Studio software, but that might be hard and I'm not sure you want to adapt the code to that output ...
written 2.3 years ago by fortin946180
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Answer: A: Compare 450k with EPIC
... We have now tested multiple functionalities of the minfi package for the analysis of EPIC arrays. We have performed a comparison of the different normalization methods in minfi, and the results are presented in our recent preprint: http://biorxiv.org/content/early/2016/07/23/065490 Hope this helps, ...
written 2.4 years ago by fortin946180
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Comment: C: Approaches for normalisation of Illumina 450k data with large global differences
... Hi Phil, this is a good reminder that we need to update the vignette of minfi (it is more than outdated). The QC line was defined using blood samples with no global hypo/hyper methylation, and therefore is not relevant for your study -- for instance most of tumor samples fall below this line in my ...
written 3.4 years ago by fortin946180
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Answer: A: 450K - "Best" Normalisation Method?
... Hi Andrew, you are corrected, depending on your dataset characteristics, some normalization methods are more appropriate than others. If the goal of your analysis is to compare different tissues, cell types, or cancers versus normals (or any other dataset with global methylation differences), you m ...
written 3.4 years ago by fortin946180
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Comment: C: Approaches for normalisation of Illumina 450k data with large global differences
... Hi Phil, I just looked at your RPubs report (pretty nice!) -- it seems indeed that you've got tighter clusters with noob. In my experience, when the sample size is small (n=19 in your study, correct?), noob by itself performs the best. However, you might want to try preprocessFunnorm() with differe ...
written 3.4 years ago by fortin946180
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Answer: A: Approaches for normalisation of Illumina 450k data with large global differences
... Hi Phil, it seems that your dataset is a perfect example of when to use functional normalization. If there are large differences in global methylation status, functional normalization should be able to keep them while removing unwanted technical variation. Functional normalization is a kosher withi ...
written 3.5 years ago by fortin946180

Latest awards to fortin946

Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Approaches for normalisation of Illumina 450k data with large global differences
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: 450K - "Best" Normalisation Method?
Good Answer 3.4 years ago, created an answer that was upvoted at least 5 times. For A: 450K - "Best" Normalisation Method?
Scholar 3.4 years ago, created an answer that has been accepted. For A: Approaches for normalisation of Illumina 450k data with large global differences
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Approaches for normalisation of Illumina 450k data with large global differences
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: 450K - "Best" Normalisation Method?
Scholar 3.4 years ago, created an answer that has been accepted. For A: Approaches for normalisation of Illumina 450k data with large global differences

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