Questions tagged [imputation]
The imputation tag has no usage guidance.
8
questions
1
vote
1answer
47 views
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....
3
votes
2answers
67 views
Block wise protein imputation
I am currently working on a dataset that contains 50 samples (10 samples * 5 blocks). The features of the date set are:
The data is perfectly balanced between blocks, with equal treatment ...
3
votes
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
803 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
299 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
150 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 ...
7
votes
1answer
174 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, ...