User: ZoeChing

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ZoeChing0
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Posts by ZoeChing

<prev • 15 results • page 1 of 2 • next >
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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 ...
batcheffect R ruv missmethyl methylation written 15 months ago by ZoeChing0
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fail to pick soft threshold in WGCNA
... Hi there! I'm trying to find the co-methylation sites using WGCNA. Methylation status were assessed using the Illumina EPIC microarray. When I run WGCNA's pickSoftThreshold() on 810135 sites (after some common preprocessing steps, such as filter out probes with bad detection P value), server kill ...
wgcna written 20 months ago by ZoeChing0 • updated 20 months ago by Kenny Westerman0
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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(patients vs healthy controls). 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 meth ...
R methylation microarray pca mds written 2.3 years ago by ZoeChing0
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Comment: A: Limma strange low p-values.
... Did u fix it? I meet the same problem. could u share some suggestions, please? ...
written 2.6 years ago by ZoeChing0
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Comment: C: strange results from differential methylation analysis using limma
... I compared those two result, only 3037 probes were the same. ...
written 2.6 years ago by ZoeChing0
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strange results from differential methylation analysis using limma
... I want to identify differentially methylated probes 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<0.05 w ...
R methylation limma written 2.6 years ago by ZoeChing0 • updated 11 weeks ago by talk2jameed0
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Comment: C: Why is a probe annotated more than one UCSC_RefGene_Group in the same gene?
... But i still confused about the method to count the distribution of DMPs. if i count as $num_TSS200=$num_TSS200+4 and $num_TSS1500=$num_TSS1500+1, it seems like i count this DMP as 5 probes. Should i took the first annotation as standard annotation (TSS200 in TAS1R1) for cg 09132215 and count as $num ...
written 2.7 years ago by ZoeChing0
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Comment: C: Why Is A Cg Island Mapped Twice To The Same Gene?
... Hi Charles, i'm processing a data from 450K beadchip to identify differentially methylated probes(DMPs) between our case and control. And i get more than 10000 DMPs. When i'm calculating the distribution of DMPs in relation to genes(such as: What percentage of DMPs located in TSS200 region), i face ...
written 2.7 years ago by ZoeChing0
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Why is a probe annotated more than one UCSC_RefGene_Group in the same gene?
... Hi, i'm processing a data from 450K beadchip to identify differentially methylated probes(DMPs) between our case and control. And i get more than 10000 DMPs. When i'm calculating the distribution of DMPs in relation to genes(such as: What percentage of DMPs located in TSS200 region), i face a quest ...
R methylation chip-seq illumina written 2.7 years ago by ZoeChing0 • updated 2.7 years ago by newbiebio80
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Comment: C: how to caculate enrichment score
... Thanks for your reply. But my OR is 0.92 (95%CI: 0.886-0.958) differs from the enrichment score in paper: enrichment score=1.09 (1.04 -1.13). I used the same input with the research, and our p values are consistent. Do i miss any steps? ...
written 2.7 years ago by ZoeChing0

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