User: ZoeChing

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ZoeChing0
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Beijing
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Posts by ZoeChing

<prev • 6 results • page 1 of 1 • next >
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Comment: C: should i include PCs or MDSs as covariates in methylation study?
... Hi Aaron. There is no difference in age, or gender between groups. All of our samples are from the same population, and PCA plot of gwas data show no population stratification in our samples. So, i thought first two MDS dimensions may correspond to the phenotype of our interest. I'm gonna remove MD ...
written 6 weeks ago by ZoeChing0
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should i include PCs or MDSs as covariates in methylation study?
... Hi there. i'm analyzing a HM450K array methylation data with 2 groups(group1 vs group2. I wanna to compare the two groups in order to find differentially methylated probes(DMPs), so, I ran limma analysis on this dataset. But when i discuss the pipeline with someone who engages in methylation data a ...
limma methylation R mds covariate written 6 weeks ago by ZoeChing0 • updated 6 weeks ago by Aaron Lun15k
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Comment: C: strange results from differential methylation analysis using limma
... Hi Gordon.  sorry i forget to mention that the "technician" using testmethod = "pooled" in IMA. And we used the same preprocessed data(666805 probes) to find DMPs, just using different methods. So, the cause of difference must in the "Find DMP" step.   We will try to use the "limma" option in IMA, ...
written 3 months ago by ZoeChing0
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Comment: C: strange results from differential methylation analysis using limma
... Well, there is no significant difference in age between  the two groups. So is the sex ratio. And all samples share the same ethnic background. You know, it's hard to control their diet and lifestyle. Considering the same ethnic background, diet or lifestyle is unlikely to be the confounding factor ...
written 3 months ago by ZoeChing0
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Comment: C: strange results from differential methylation analysis using limma
... Hi Aaron, thanks for your advice. Yes, the gender and group were two-level categorical variables and the Age is continuous variable. I have tried to add trend=TRUE and robust=TRUE option in  eBayes, but it failed to make a big difference. At this time, i used beta value instead of M values. Without ...
written 3 months ago by ZoeChing0
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strange results from differential methylation analysis using limma
... I want to identify differentially methylated probes(DMPs) between two groups.  After preprocessed raw data, 666805 probes remained. Differential methylation analysis was performed on the remain probes using limma. Age and gender information were used as covariates. Probes with BH adjusted P value&l ...
limma methyanalysis methylation ima written 3 months ago by ZoeChing0 • updated 3 months ago by Gordon Smyth30k

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