Braulio Mark Valencia

7 Questions 9 Answers 0 Followers

Questions related from Braulio Mark Valencia

How to get the annotation file of the Immunochip array?

Dear community, I'm inputting data from an old GWAS study based on the Immunochip array, and I need the annotation file to conduct a few QC steps. I can't find it on the Illumina website; I...

07 April 2024 8,932 2 View

What's the most reliable/available source of GWAS data from South Asian countries?

Hi everyone! I'm looking for accessible GWAS data from South Asian countries as I need to verify the quality of data obtained from a Sri Lankan cohort using the UK biobank array. After all the...

04 May 2023 5,052 0 View

How to find biologic effect of specific mutations in Dengue genomes (i.e. aminoacid level or antigenic properties once folded)?

Hi all! I have found specific mutations in dengue genome sequences apparently related to the infection outcome. Here my questions: How can I find if this mutation is synonymous or...

25 July 2022 3,122 2 View

Is cos2, coord, or contrib equivallent to loading when doing PCA?

Hi there, I've been using FactoMineR to run PCA. I tried other packages but due to the nature of my data, this is the most suitable. I have done PCA in Stata and the individual scores (loadings?)...

17 April 2022 2,456 6 View

What's the role of SNPolisher for getting ready-to-use UK biobank data?

Hello everyone! I have finished all the APT steps on my UK biobank CEL files. I understand that once this is done, SNPolisher should be used to verify the quality of probes/SNPs and also extract...

18 March 2022 975 0 View

Using SNPolisher - how the *.CEL files are used to obtain QC metrics?

Hello! I recently received many *.CEL files from a recent UK biobank genotyping. According to the SNPolisher guide, I have to conduct certain metrics on these SNPs to keep just the ones fulfilling...

14 October 2021 3,942 1 View

How can I create my PED/MAP files for PLink from scratch?

Hello everybody! I'm working in a candidate gene association study, and I'm planning to use PLINK for that purpose. My samples have been sequenced, but the report just provided me with the list of...

06 August 2019 2,706 3 View