Questions tagged [imputation]

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REMC SNP annotations for transcriptome prediction - epiXcan

I have been trying to use a pipeline for predicting gene expression for a target gene (Although you can do it for many) - the name of this method is epiXcan. Here is a link to the paper: https://www....
2
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0answers
54 views

Block wise protein imputation

I am currently working on a dataset that contains 50 samples (10 samples * 5 blocks). The data is perfectly balanced between blocks, with equal treatment representation in each block. Each block ...
3
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1answer
46 views

Impute phenotype under some constraints

Errors happen frequently in the lab and I got one sample that we mixed one important information (the region of the sample) between two samples. Now we don't know which sample is from which region, ...
3
votes
2answers
1k views

How to filter info score post-imputation?

this is a very basic question, but I cannot find it explicitly stated anywhere: When exactly should I filter the info scores after imputation? I did imputation in Impute2 and am planning on using ...
5
votes
1answer
681 views

Order of batch effects removal, data imputation and library size normalization in scRNA-seq data

I am preprocessing scRNA-seq data. What is the best practice in use to run both ComBat for batch effects removal, data imputation (to mitigate dropout) and library size normalization? I thought that ...
4
votes
1answer
298 views

Recommendations for missing value imputation - DNA methylation data

I'm looking for some options for imputation for a high-dimensional dataset of DNA methylation (bisulfite sequencing) data. Dimensions on the order of 50-100 samples x ~500,000 CpG loci/features. I'...
7
votes
1answer
141 views

Imputing missing genotypes from separate genotyping panels

What is the current standard for imputing missing genotypes between two genotyping panels? I have two populations genotyped using two different panels (A & B), and I would like to impute all the ...
6
votes
1answer
170 views

Filtering imputed GWAS SNPs based on a MAF difference of 10%

There are many posts on the web regarding QC steps pre and post-imputation. Does applying below (new?) 10% MAF difference rule make sense, pitfalls? Here is the process: Get MAF for imputed set, ...