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User: Bioinformatics_NewComer

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Posts by Bioinformatics_NewComer

<prev • 125 results • page 1 of 13 • next >
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Comment: C: How to adjust data for "continuous" covariates ?
... ## ... Now use lm1$residuals instead of dat$y Would you please be able to explain Why this residuals are used as new phenotype and how? ...
written 3 months ago by Bioinformatics_NewComer • 320
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R - snpmatrix - data filtering
... Hi all, I'm interested to use genegeneinteraction R package. For that data are read and a snp matrix is generated. When I try to run gene gene interaction I get error GGI.res <- GGI(Y=Y, snpX=data$snpX, genes.info=data$genes.info,method="PCA") Error: > Error in GGI(Y = Y, snpX = data ...
matrix snp written 7 months ago by Bioinformatics_NewComer • 320
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Comment: C: Help with SnpMatrix in R
... The link is dead. Am too looking for help with snpmatrix. ...
written 7 months ago by Bioinformatics_NewComer • 320
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Comment: C: Module merging WGCNA
... URL: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/Consensus-NetworkConstruction-man.pdf Section 2.a.7, Page 9, merge = mergeCloseModules(multiExpr, unmergedLabels, cutHeight = 0.25, verbose = 3) Here, code merges modules that have close/similar expre ...
written 8 months ago by Bioinformatics_NewComer • 320
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Comment: C: Module merging WGCNA
... I'm working step by step, looking into function parameters and reading explanations provided on the tutorial. After rummaging and lost I've posted my query. I can share code and comments if needed to show my inputs. https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tut ...
written 9 months ago by Bioinformatics_NewComer • 320
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Module merging WGCNA
... Hello all, I'm interested to perform gene co-expression using WGCNA R module. I clean data for samples and remove genes that don't form any cluster. Post cleaning I perform clustering to identify different modules (40 excluding grey). Each module consist different number of genes, I generate list o ...
wgcna expression microarray written 9 months ago by Bioinformatics_NewComer • 320
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Comment: C: VCF file lacks alternative allele listing for most rs ids
... Can anyone assist with this? Why does this happen. I've ~6K snps with no alternate allele(s) on CHR22 for one of the callings I did. GrCH37, Homo Sapiens, Illumina hiseq 150 bp. ...
written 9 months ago by Bioinformatics_NewComer • 320
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Comment: C: 16S rRNA classification pipeline
... Which region do you've for 16S? Also, there's no assembly needed for 16S data. Do you've Illumina data? ...
written 10 months ago by Bioinformatics_NewComer • 320
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Comment: C: Calculate heterozygosity for each SNPs in the bim file.
... > Error: Failed to open Colli_buffalo_diversity.map You have binary format (bim/bam files) acceptable by plink. Use ***--bfile*** ...
written 10 months ago by Bioinformatics_NewComer • 320
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Comment: C: Please help with Eagle
... If you're working with CHR9, it could be good to work with genetic map for CHR9 only. ...
written 11 months ago by Bioinformatics_NewComer • 320

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