User: ghmdsr

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ghmdsr40
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2 years, 6 months ago
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Posts by ghmdsr

<prev • 10 results • page 1 of 1 • next >
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Extracting data from psimitab format
... I want to use InWeb_InBioMap PPI database in R or python. The format of this data is PsimiTab format. Previously I used STRING score. In case of STRING ppi db, they provide a package which can help us using that in R interface. With InWeb_InBioMap PPI db, I want to handle this data and use this ...
software error R rna-seq written 2.2 years ago by ghmdsr40
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(Closed) getting raw count data related to kinase inhibitor
... I want to get raw count data which is related to kinase inhibition. Specially, I want to analyze DEG between two groups, one is treated kinase inhibition drug the other isn't. Where can I get? ...
gene rna-seq written 2.2 years ago by ghmdsr40
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how can i get normalized gene expression matrix in TCGA?
... i want to run an algorithm. The algorithm calculates TF activities score per sample,. The algorithm says ' Input needs a normalized gene expression matrix'. so I tried to get normalized gene expression matrix, 1. TCGA breast cancer raw count from GDAC. 2. sample-wise normalization ( TMM/ limma voo ...
gene rna-seq written 2.2 years ago by ghmdsr40 • updated 2.2 years ago by Biostar ♦♦ 20
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What information in dispersion plot using edgeR?
... I m doing DEG analysis using edgeR. I have some questions. 1. Difference between 'edgeR' and 'Limma' 2. Interpreting 'dispersion plot' : after estimating dispersions Code: dgList2 <- estimateGLMCommonDisp(dgList1,design = designMat) dgList3 <- estimateGLMTrendedDisp(dgList2, ...
gene R tutorial rna-seq written 2.4 years ago by ghmdsr40 • updated 2.4 years ago by h.mon31k
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TMM normalization using tweeDEseq
... I want to normalize gene expression values per sample . In doing this, TMM normalization is necessary. My data is WTS data which is consist of raw count. And there are 32 samples. Some of them are response group and the others are non-response group. My question : 1. I think TMM normalization ...
gene rna-seq written 2.4 years ago by ghmdsr40
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Tutorial: (Closed) raw count data- normalization
... I got raw count data,which would consist of 32 samples and 20000 genes. With this data, I have to normalize this. first step; normalized gene expression values per sample. second step: gene-wise normalization Question1 : what is gene-wise normalization? Question2 : how can i this two step? Q ...
gene tutorial rna-seq written 2.4 years ago by ghmdsr40
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raw count data- normalization
... I got raw count data,which would consist of 32 samples and 20000 genes. With this data, I have to normalize this. first step; normalized gene expression values per sample. second step: gene-wise normalization Question1 : what is gene-wise normalization? Question2 : how can i this two step? ...
gene tutorial rna-seq written 2.4 years ago by ghmdsr40 • updated 2.4 years ago by Biostar ♦♦ 20
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If genes in one gene set are abundant in top, bottom of ranked list?
... Let's suppose that there are 100 genes in one specific gene set and 20000 genes are used in making ranked list. 50 genes in the gene set are located in top of ranked list(pvalue very low,sign of fold-change= +), and the other 50 genes are located in the bottom of ranked list.(pvalue very low, sig ...
gene rna-seq written 2.4 years ago by ghmdsr40 • updated 2.4 years ago by Zhilong Jia1.6k
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How can I get test data (raw count) for my algorithm?
... Hi I'm first year graduate student. I make an algorithm, so I want to test my algorithm ... but i don't know where I can get it. Input data for my algorithm is transcriptome data. I need raw count data, (especially, about kinase amplification) Please let me know where I can get raw count data. ...
rna-seq written 2.5 years ago by ghmdsr40 • updated 2.5 years ago by zx87549.7k
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how to interpret NES(normalized enrichment score)?
... hi i'm first-year graduate student. I got the result of my analysis in which NES is included. I wonder about the meaning of positive score/negative score of NES. I know that NES negative score means weaker relative activity in a sample compared with the background population, and positive score ...
gene R rna-seq written 2.5 years ago by ghmdsr40 • updated 21 months ago by johnsonnathant80

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Popular Question 2.0 years ago, created a question with more than 1,000 views. For how to interpret NES(normalized enrichment score)?

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