User: ZoeChing

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ZoeChing0
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Posts by ZoeChing

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which value from ruvadj in missMethyl can present methylation status
... HI there! i am working with 100 sample of  850K methylation data. After probe filter and normalization, SVD plot indicate that batch effect (including slide and array) has an impact in methylation status. Unfortunately, Slide is confounded with SampleGroup (the factor of our interest). So i cannot ...
methylation batch effect ruv missmethyl written 10 months ago by ZoeChing0
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Comment: C: failed to use multiple threads in R via openblas
... Hi martin,thx for your reply. i had re-installed R and configured with --with-blas="-lopenblas . After installation, i executed“./R” from the “bin” directory. "lsof -p pidID |grep blas " reports R is using libopenblas-r0.2.19.so, but still only 1 thread.  btw, i have set  export OPENBLAS_NUM_THREA ...
written 21 months ago by ZoeChing0
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failed to use multiple threads in R via openblas
... i was trying to make network construction in wgcna packages execute faster. As recommended in the "frequently asked questions" ,  i wanna to compile R with blas library.  After openblas installation completed, i found the following information in the manual : "Once installed it canbe used by someth ...
wgcna R openblas blas threads written 21 months ago by ZoeChing0 • updated 21 months ago by Martin Morgan ♦♦ 23k
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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 22 months 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 22 months ago by ZoeChing0 • updated 22 months ago by Aaron Lun23k
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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 24 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 2.0 years 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 2.0 years 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 2.0 years ago by ZoeChing0 • updated 2.0 years ago by Gordon Smyth36k

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