User: Maxime Lamontagne

Reputation:
2,210
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Location:
Québec
Website:
http://www.criucpq.ula...
Last seen:
5 months, 3 weeks ago
Joined:
8 years, 11 months ago
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b*********@gmail.com

Posts by Maxime Lamontagne

<prev • 152 results • page 1 of 16 • next >
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Comment: C: How to run PLINK from a personal computer
... Could you post your command. ...
written 2.4 years ago by Maxime Lamontagne2.2k
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Comment: C: How to run PLINK from a personal computer
... First, try PLINK 1.9 : [https://www.cog-genomics.org/plink/1.9/][1] [1]: https://www.cog-genomics.org/plink/1.9/ ...
written 2.4 years ago by Maxime Lamontagne2.2k
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Comment: C: PLINK .bim file shows chromosome 0 on Affymetrix chip
... Did you try the --exclude option in PLINK? ...
written 2.6 years ago by Maxime Lamontagne2.2k
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Comment: C: What people do with the probes that doesn't have any GENE SYMBOL in annotation d
... I think this paper is doing exactly what you want. > Framework for reanalysis of publicly available Affymetrix® GeneChip® > data sets based on functional regions of interest https://www.biorxiv.org/content/biorxiv/early/2017/04/11/126573.full.pdf ...
written 2.6 years ago by Maxime Lamontagne2.2k
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Answer: A: What does people do with the probes that doesn't have any GENE SYMBOL in annotat
... It’s not unusual in older array. Due to changes in gene annotation and reference sequence, some probe set may be outdated (probes not mapping to any gene in the new build). To find a gene for your probe set, you need to blat all the probes of the probe set and look where they are mapping. ​ ...
written 2.7 years ago by Maxime Lamontagne2.2k
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Answer: A: literature review by a web server
... [IBioGuide][1] could hep you. [1]: https://www.advaitabio.com/ibioguide.html ...
written 2.7 years ago by Maxime Lamontagne2.2k
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Answer: A: logistic regression with PLINK
... Maybe the "--freq" command will give you this info. ...
written 2.8 years ago by Maxime Lamontagne2.2k
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Comment: C: Using Plink, get allele frequencies for a subset of individuals
... I gues one of your file is incorrectly formatted. If you want, I could take a quick look at them. ...
written 2.8 years ago by Maxime Lamontagne2.2k
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Comment: C: Using Plink, get allele frequencies for a subset of individuals
... Try this : ./plink --file /path/in_data --chr 1-22 --allow-extra-chr --keep NewFile.txt --make-bed --out Temp1 --allow-no-sex ./plink --bfile Temp1 --pheno /path/cases.txt --freq --out out_data_case --allow-no-sex ...
written 2.8 years ago by Maxime Lamontagne2.2k
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Answer: A: Using Plink, get allele frequencies for a subset of individuals
... Create a file with only the FID and IID of the subjects you want to keep (NewFile.txt). Then try this : ./plink --file /path/in_data --chr 1-22 --allow-extra-chr --keep NewFile.txt --pheno /path/cases.txt --freq --make-bed --out out_data_case ...
written 2.8 years ago by Maxime Lamontagne2.2k

Latest awards to Maxime Lamontagne

Scholar 2.1 years ago, created an answer that has been accepted. For A: Plink MAF Calculation
Good Question 2.1 years ago, asked a question that was upvoted at least 5 times. For Bioinformatic Cartoon
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: What does people do with the probes that doesn't have any GENE SYMBOL in annotat
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Plink: Quick Way To Combine Two Datasets Using Only Common Markers
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Plotting Human Karyotype - Software
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Computing: A Vision For Data Science
Scholar 2.1 years ago, created an answer that has been accepted. For A: How to tell Plink to merge based on Hg19 coordinates, not based on SNP ID
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Automatic Ld Plot For Multiples Snps On Different Chromosome
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Accounting for problem SNPS when merging multiple plink files
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Plink: Quick Way To Combine Two Datasets Using Only Common Markers
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: Accounting for problem SNPS when merging multiple plink files
Scholar 2.7 years ago, created an answer that has been accepted. For A: Plink MAF Calculation
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Scholar 3.0 years ago, created an answer that has been accepted. For A: Plink MAF Calculation
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Plink: Quick Way To Combine Two Datasets Using Only Common Markers
Good Answer 3.3 years ago, created an answer that was upvoted at least 5 times. For A: Minor allele frequency calculation
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Appreciated 3.8 years ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink

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