Phụng Dương

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Questions related from Phụng Dương

Problems with QQ plot for GWAS?

Hi everyone, I am carryied out a GWAS with the sample size about 5000 control versus 5000 cases, and 260,000 variants at the beginning After the quality control with MAF at 0.05, I achieved only...

12 December 2019 6,752 3 View

How to combine fold change in microarray meta-analysis?

Hello, I would like to calculate the foldchange of differentially expressed genes after I meta-analyzed 9 datasets. I have calculated the fold change of those genes in each datasets but I wonder...

31 May 2019 535 3 View

How to do validation after doing normalization in microarray?

During meta-analysis, we have to do normalization data in preprocessing data steps and then we will analyze the different expressed genes. But after we do the normalization, how can we know that...

19 December 2018 861 4 View

Normalization in microarray: what is the difference between log2 transformation and calculating log2 ratio in the primary step?

I am studying about how to do normalization. At first, I think that people have to calculate the log2 ratio as a primary step to convert the T=R/G ratio in microarray into another simple number to...

18 December 2018 2,734 2 View

Beside pH and temperature, are there any other factors effect on the activity of xanthine oxidase?

Beside pH and temperature, are there any other factors effect on the activity of xanthine oxidase such as light, concentration or any else? Please give me some suggests and more details. Thanks so...

29 February 2016 9,446 2 View

How should we do for test heterogenity for microarray meta-analysis?

I am learning microarray meta-analysis and heterogenity is a really essential test after we carry out meta-analysis. However, there are some points that I still do not understand: 1. There are 3...

01 January 1970 597 2 View

Why do we need perfect probe and mismatch probe to do microarray?

In microarray, there are 2 types of probes. I wonder why we need to use mismatch probe to know the gene expression? In addition, considering mutation, the substitution nucleotide can be vary a lot...

01 January 1970 2,159 6 View

Is there a unit for gene expression?

Hello, there are so many ways to analysis the expression of gene and mRNA, but I wonder if we have a general unit to specific the expression of a gene (and this unit can use for all of methods)? I...

01 January 1970 5,241 2 View

Effect sizes and standard error?

Hello, I have read a paper about how to carry out meta-analysis in 5 datasets of microarray. The method they used is combing effect sizes. After they calculate the pooled effect size, they...

01 January 1970 9,721 4 View