User: Sam

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Sam3.0k
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Posts by Sam

<prev • 442 results • page 1 of 45 • next >
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Answer: A: liftOverPlink Syntax error
... From the look of it, your liftOverPlink.py might be a html file. Could you please make sure you have downloaded the file correctly? Maybe this link will help https://github.com/sritchie73/liftOverPlink/archive/master.zip ...
written 5 hours ago by Sam3.0k
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Answer: A: Command to download "Height" information from UKB with ukbfetch
... You will need to follow the instruction [here][1] starting from page 8. You will need the md5 password to be able to access the data (which should be attached in an email sent to the PI of the UKB application). After you've got the encrypted data, you can convert it to R format or csv format using u ...
written 7 days ago by Sam3.0k
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Answer: A: How to understand Instance and Array in UKB phenotype data
... Array is for fields that can have multiple entries e.g. ICD10. It is basically breaks down the array into multiple file. For example, if someone has 20 ICD code, then those 20 ICD code will be found in 10 different array files. Instance is something related to the multiple measurement. Some of the ...
written 8 days ago by Sam3.0k
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Answer: A: p value from multiple columns using R??
... Using data.table (assuming your data is called dt), you can do a t.test on each row with the following code. Though as others have suggested, you should really think about your experimental design and use the appropriate statistic model, otherwise you will just get meaningless p-values. librar ...
written 9 days ago by Sam3.0k
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Comment: C: p value from multiple columns using R??
... Does that mean you want row 1 compare with all other rows, the repeat? Or are you comparing S1 vs S2, S1 vs S3, ..., S5 vs S6? ...
written 10 days ago by Sam3.0k
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Comment: C: Validatingm Polygenic Risk Scores from PRSice
... Negative beta isn't a problem. you can view effective allele with negative beta as "protective", which is alright. ...
written 13 days ago by Sam3.0k
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Comment: C: Validatingm Polygenic Risk Scores from PRSice
... You can use the --perm option, which will generate an empirical p-value for you (preferably --perm 10000 or above). If empirical p-value is less than 0.05, then you are good to go. (but do note that the R2 is still inflated as you are not doing out of sample validation) ...
written 14 days ago by Sam3.0k
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Comment: C: Validatingm Polygenic Risk Scores from PRSice
... The 1000 Genome data can be used as the reference. The usage and requirement for the `--ld` flag is exactly the same as the `--target` flag. You will need the plink or bgen file. Unfortunately, yes, with your sample size, you will need to think of something clever to have a hope of getting anythin ...
written 14 days ago by Sam3.0k
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Answer: A: Validatingm Polygenic Risk Scores from PRSice
... Your sample size is simply too small. That will usually not give you any reasonable result. I suspect that as you've less than 100 samples, the clumping LD varies quite a lot, lead to more variants being removed than normally would (which lead to the small variant count). One way to get around that ...
written 17 days ago by Sam3.0k
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Answer: A: Pathway and gene analysis based on GWAS results
... You can try out [MAGMA][1], which is one of the most popular tool for pathway analysis on GWAS results [1]: https://ctg.cncr.nl/software/magma ...
written 18 days ago by Sam3.0k

Latest awards to Sam

Scholar 13 days ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Scholar 6 weeks ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Scholar 3 months ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Appreciated 3 months ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
Epic Question 7 months ago, created a question with more than 10,000 views. For Normalization Of Rna Sequencing Counts (By Ercc / Gene Length)
Scholar 7 months ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Scholar 9 months ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Scholar 10 months ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Popular Question 13 months ago, created a question with more than 1,000 views. For Method for analyzing Targeted re-sequencing based on Ligation Mediated PCR?
Appreciated 17 months ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Student 21 months ago, asked a question with at least 3 up-votes. For Interpretation Of Differential Exon Usage Results
Great Question 22 months ago, created a question with more than 5,000 views. For Piping Markduplicates
Popular Question 2.4 years ago, created a question with more than 1,000 views. For High Kmer Content in middle of the read
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: High Sequence Duplication levels in FastQC
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: difference between assembly hg19 and GRCh37
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Popular Question 3.2 years ago, created a question with more than 1,000 views. For High Kmer Content in middle of the read
Popular Question 3.5 years ago, created a question with more than 1,000 views. For RNA Sequencing Pooling design and statistic analysis
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practic
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
Great Question 3.8 years ago, created a question with more than 5,000 views. For Normalization Of Rna Sequencing Counts (By Ercc / Gene Length)
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
Commentator 4.5 years ago, created a comment with at least 3 up-votes. For C: Merge 4 Fastq Files

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