User: ZoeChing

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ZoeChing0
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Posts by ZoeChing

<prev • 13 results • page 1 of 2 • next >
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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 7 months 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 10 months 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 10 months 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 10 months ago by ZoeChing0
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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 11 months 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 11 months 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 11 months ago by ZoeChing0 • updated 11 months 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 11 months ago by ZoeChing0
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how to caculate enrichment score
... Hi there, i am processing a genome-wide methylation data, and i wanna to find out which chromosome were enriched with differentially methylated probes(dmp). I noticed a research compared the distribution of dmps located on each chromosome. > for example, 8.87% of CpG probes on Chromosome 13 we ...
R fisher written 11 months ago by ZoeChing0
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Comment: C: Plugin 'dbNSFP' of VEP went wrong
... OK. Thx for your help. ...
written 14 months ago by ZoeChing0

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