User: Apprentice

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Apprentice20
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Posts by Apprentice

<prev • 37 results • page 1 of 4 • next >
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Sex inconsistency in 1000 genomes phase 3 TSI samples
... Hi. I'm going to check sex consistency using 1000 genomes phase 3 TSI samples. As a result, inconsistency in sex was detected in 3 samples. The IDs were NA20506, NA20530, and NA20533. So, I would like to know that this inconsistency was often know? Should I removed the samples in chrX SNP analysis? ...
snp written 15 days ago by Apprentice20 • updated 14 days ago by chrchang5235.0k
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How to convert DS value for chrX non-PAR SNPs in male
... Hi. I have imputed male data of SNPs located on chrX non-PAR (pseudo autosomal region) using 1000 genomes phase 3 as a refrence. The imputation was performed by using minimac3. The imputed genotypes have GT, DS, and GP information. The DS data is ranging from 0 to 1. In many X-wide association s ...
imputation snp chrx par written 7 weeks ago by Apprentice20
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Comment: C: Determination of haplotypes based on genotype data of 2 SNPs
... Thank you for your advice. But I would like to know how to determine haplotypes for each individual. Could you give me any advice about it? ...
written 10 weeks ago by Apprentice20
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Determination of haplotypes based on genotype data of 2 SNPs
... Hi. I would like to determine haplotypes based on genotype data of 100 patients with 2 SNPs. I know that PHASE software can determine haplotypes based on genotype data of many SNPs. Can this software determine haplotypes based on genotype data of two SNPs? If it is impossible. Could you tell me o ...
snp written 11 weeks ago by Apprentice20
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Comment: C: How to export a network of a specific module to Cytoscape
... Thank you for your advice. I did it! ...
written 3 months ago by Apprentice20
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Comment: C: How to export a network of a specific module to Cytoscape
... Thank you for your kindly comments. I could know that the adjacency matrix was needed to do exportNetworkToCytoscape. However, I can't find how to get the adjacency matrix from expression data in the multi-set format. The link, which you suggested, explains how to get the adjacency matrix from exp ...
written 3 months ago by Apprentice20
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Comment: C: How to export a network of a specific module to Cytoscape
... Thank you for your quick reply. I have tried to use the exportNetworkToCytoscape function as below. --------------------------------- mods = blockwiseConsensusModules(multiExpr, maxBlockSize = 30000, corType = "bicor", power = STPowers, networkType = "signed hybrid", TOMDenom = "mean" ...
written 3 months ago by Apprentice20
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How to export a network of a specific module to Cytoscape
... Hi I constructed a consensus network based on six data sets of gene expression profiles. To construct the network, I used blockwiseConsensusModules function of WGCNA package. And then, I extracted a module associated with outcome from the network. Because I would like to draw a network of the modu ...
wgcna gene expression written 3 months ago by Apprentice20
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Answer: A: AttributeError: 'dict' object has no attribute '__NUMPY_SETUP__' in install of P
... Hi My problem was solved by doing below command. # pip install -r requirements.txt # python setup.py install Thank you for advices. ...
written 7 months ago by Apprentice20
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Answer: A: AttributeError: 'dict' object has no attribute '__NUMPY_SETUP__' in install of P
... I attached an error message file about this problem. Please give me any advices if you noticed. https://github.com/brielin/Popcorn/files/2440225/log.txt ...
written 7 months ago by Apprentice20

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