User: rednalf

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rednalf20
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Posts by rednalf

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Comment: A: Obtain genotype data from Eurasian and HapMap populations
... Sure, it is Supplementary Figure 21 of https://www.nature.com/articles/s41590-018-0049-7 ...
written 11 days ago by rednalf20
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Comment: C: Obtain genotype data from Eurasian and HapMap populations
... Thank you Kevin for your answer. I have been doing PCAs using 1KG data (CEU, GIH, MEX, TSI, YRI, etc.) and your tutorial (thank you btw), but since my cohort is French I was interested in plotting my samples with cohorts with a more precise ancestry (only Eurasians) to see if they overlap with Frenc ...
written 11 days ago by rednalf20
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Obtain genotype data from Eurasian and HapMap populations
... I have seen this figure in a Nature Immunology paper. I was wondering where I can find the genotype data from the 36 populations (32 Eurasian populations and 4 HapMap populations) in panel b. Do you know if it is open access? I couldn't find anything online. ![Nature Immunology Figure][1] [1] ...
genome snp written 11 days ago by rednalf20
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Yeo-Johnson and Logarithmic transformation
... Is a Yeo-Johnson transformation using a lambda equal to 0 the same transformation as a logarithmic transformation? ...
R transformation yeo-johnson logarithm statistics written 11 weeks ago by rednalf20 • updated 11 weeks ago by Kevin Blighe24k
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Comment: C: Inverse normal transformation
... Yes a lot, thank you very much for your (fast) help! ...
written 11 weeks ago by rednalf20
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Comment: C: Inverse normal transformation
... I found it in the Supplementary Information, page 18 (https://media.nature.com/original/nature-assets/nature/journal/v490/n7419/extref/nature11401-s1.pdf) ...
written 11 weeks ago by rednalf20
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Comment: C: Inverse normal transformation
... Thank you. I have considered log, square root, cube root and Johnson transformation for now. I will have a look at DESeq2. What do you think about the inverse normal transformation and the script based on Yang et al.'s paper? ...
written 11 weeks ago by rednalf20
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Comment: C: Inverse normal transformation
... Thank you for your comment - the information has been added to the initial post. ...
written 11 weeks ago by rednalf20
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Inverse normal transformation
... My phenotype is not normally distributed. I tried several transformations but none of them seems to improve the normality. I am now interested in an inverse normal transformation using R. Is something like the following correct, x being my phenotype? qx <- qnorm((rank(x)-0.5)/sum(x)) It ...
R inverse transformation statistics written 11 weeks ago by rednalf20
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Log-tranformation and GWAS
... Before doing any GWAS (genome-wide association study) it is necessary to check for the normality of the phenotypic distribution. If the phenotype is normally distributed only once it is log-transformed, what phenotypic data do I have to use while doing the GWAS? The non-transformed one or the log-tr ...
gwas transformation genotype logarithm statistics written 11 weeks ago by rednalf20 • updated 11 weeks ago by Kevin Blighe24k

Latest awards to rednalf

Popular Question 9 weeks ago, created a question with more than 1,000 views. For PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
Popular Question 17 months ago, created a question with more than 1,000 views. For PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values

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