Braulio Mark Valencia

10 Questions 10 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 9,047 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 5,120 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 3,198 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 2,521 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 1,043 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 4,003 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 2,770 3 View

How can I access to the CEPH Utah SNPs datasets?

Dear Researchers! I am doing research looking for SNPs associated with parasitic infections. One SNP in which I am interested in is the rs2043211. This is a nonsense mutation in the CARD8 gene....

27 February 2019 738 1 View

Alanine/proline supplementation for improvement of Leishmania culture?

Good morning! I'm interested to improve recovery of Leishmania parasites from conventional NNN cultures obtained from tegumentary samples. Based on this publication...

17 August 2016 915 2 View

Are there differences in parasite load between OWCL and NWCL?

Hello researchers! I'm trying to verify if there is objective evidence showing differences in PL between OWCL and NWCL. I remember a discussion with a college from Sudan about this topic and I...

01 January 1970 8,903 0 View