User: lanjinglingxiaoni

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Location:
Singapore
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4 years, 10 months ago
Joined:
5 years, 9 months ago
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l****************@gmail.com

Posts by lanjinglingxiaoni

<prev • 6 results • page 1 of 1 • next >
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Comment: C: the meaning of "NA" in plink meta-analysis result
... thank you very much. `+qt` is important ...
written 5.7 years ago by lanjinglingxiaoni20 • updated 26 days ago by RamRS25k
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the meaning of "NA" in plink meta-analysis result
... Hi, I use the meta-analysis function in PLINK to meta analyze two cohorts. For example Cohort1: SNP     CHR    BP            pvalue         beta            se     rs7412    19    45412079    4.80e-13    -.544908    .0753598     Cohort2   SNP     CHR    BP            pvalue         beta       ...
meta association na plink written 5.7 years ago by lanjinglingxiaoni20 • updated 5.7 years ago by chrchang5236.4k
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How does "missing" (3rd column) of sample file in SNPTEST affect the results?
... I have a question regarding the MISSING column (3rd column) of SAMPLE file for SNPTEST. In the webpage of SNPTEST (http://www.stats.ox.ac.uk/~marchini/software/gwas/file_format.html), it said that:  The sample file has three parts (a) a header line detailing the names of the columns in the file, ( ...
sample file gwas snptest imputation missing written 5.8 years ago by lanjinglingxiaoni20
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Comment: C: how to do Mantel extension test for SNP allele frequency among different cohort
... the other similar case: a paper published in Nature http://www.nature.com/nature/journal/v447/n7145/full/nature05911.html#B5 in the section "control group" ...
written 5.8 years ago by lanjinglingxiaoni20 • updated 5 weeks ago by RamRS25k
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how to do Mantel extension test for SNP allele frequency among different cohort or different batch or different chip
... In this paper (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0067650), 3000+ subjects were genotyped by two/three different chips. They used Mantel extension test to identify high discrepancy allele frequency of SNPs, which may due to chip/batch effect, e.g 0.30 in chip A, 0.21 ...
R snp mantel gwas written 5.8 years ago by lanjinglingxiaoni20
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Comment: A: Question About Gwas And Shared Controls.
... May I know how to do Mantel-extension test for differences in allele frequencies of SNPs? I have read some materials but I am still very confused about how to prepare the data and which variable correspond to which one? I am too desperate to ask here......... Thanks ...
written 5.8 years ago by lanjinglingxiaoni20 • updated 5 weeks ago by RamRS25k

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