User: ytian

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ytian0
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Posts by ytian

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Answer: A: Duplicate gene names in count matrix from GTF file that can't be parsed to edgeR
... I think you can make a list of those duplicate genes with down below codes (I assume your matrix with gene symbol as colnames) >n_occur <- data.frame(table(Data$Columns)) >n_occur[n_occur$Freq > 1,] Then you can proceed to locus information or coding length to verify your gene list ...
written 21 months ago by ytian0
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Error when using "Module_A.r" of TCGA-assembler
... Dear everyone I use TCGA assembler to retrieve some data. But when I tried Methylation 450K data. The code i used are: filename_READ_Methylation450 = DownloadMethylationData(cancerType = "LUAD", assayPlatform = "methylation_450", saveFolderName = "./Methyl",inputPatientIDs = rownames(LUAD.ID)) I ...
R written 23 months ago by ytian0 • updated 22 months ago by Biostar ♦♦ 20
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Comment: C: Aggregating Gene Expression Across Rows
... Sorry. The MMAD method I mentioned is list below https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btt566 But they give few detail about the imput data format or instruction. ...
written 24 months ago by ytian0
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Comment: C: Aggregating Gene Expression Across Rows
... Awesome Ryan, I am doing the "look at the level of contamination in samples of non-targeted tissues" recently. And I want to ask whether it is possible to remove these contamination. I just know we can calculate a gene set score for each patient and I have no idea about the subsequent solution. Can ...
written 24 months ago by ytian0
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Copy number analysis by Golden Helix
... Dear everyone I recently focused on the copy number analysis using SNP numeric data produced by illumina 2.5M platform. I have several questions for statistical experts who have experience in calculating the copy number by the SVS function CNAM which mainly creates a segment means to represent genom ...
genome snp written 2.0 years ago by ytian0 • updated 4 months ago by Gabe Rudy310

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