User: wildist

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wildist0
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Posts by wildist

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Comment: C: qsea non-TCGA 450K Human Methylation Calibration Dataset
... Hello Matthias, Thank you for your reply. The problem is persists. I will start another thread after summarise what we get. Best, Walter ...
written 8 weeks ago by wildist0
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Comment: C: qsea non-TCGA 450K Human Methylation Calibration Dataset
... Hello Matthias, After update qsea to 1,10, I found problem in loading bam file into analysis. It happens in the addCoverage step which has following error code: [W::bam_hdr_read] bgzf_check_EOF: No error Error in lapply(ReadsL, "names<-", fields) : 'names' at ...
written 9 weeks ago by wildist0
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Comment: C: qsea non-TCGA 450K Human Methylation Calibration Dataset
... Solved. Thank you Best, Walter ...
written 3 months ago by wildist0
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Comment: C: qsea non-TCGA 450K Human Methylation Calibration Dataset
... Hello Matthias,          Thank you for your reply. We finally complete the first set of analysis by using qsea and bisulfites sequencing has been used to confirm some DMR. It really works. In next stage, I want to use clustering method to see if there is any molecular subtype of the disease. I woul ...
written 12 months ago by wildist0
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Comment: C: qsea non-TCGA 450K Human Methylation Calibration Dataset
... Hello,         The error has been solved. But I have encountered another one. I successfully added the normalization file for calculation. Then I compared the data with/without normalization which give me the same number of windows (500bp each). I used nfpkm instead of beta as the norm_method. I wo ...
written 14 months ago by wildist0
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qsea non-TCGA 450K Human Methylation Calibration Dataset
... Hello,          I am using qsea to study the methylome in paediatric cancer. Since TCGA does not provide such calibration data, I have to do it myself. I mimic the tutorial example to create a Granges object contain all 450k probe data. After executing qseaSet=addEnrichmentParameters(qseaSet, enric ...
qsea written 14 months ago by wildist0 • updated 14 months ago by Matthias Lienhard140

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