User: DataFanatic

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DataFanatic100
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Posts by DataFanatic

<prev • 72 results • page 1 of 8 • next >
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Answer: A: differential gene expression analysis
... Devon, How can I plot the data going into the analysis? design<-model.matrix(~group+batch+RIN) will include RIN in the model and this should change the way samples cluster by PCA or MDS plot. Is there a way to extract the corrected counts matrix? Thank you! ...
written 5 weeks ago by DataFanatic100
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Comment: A: differential gene expression analysis
... Is there a way to visualize the data (residuals) using PCA or MDS plot after performing the linear modeling? I want to do this to confirm the samples no longer cluster by batch. ...
written 5 weeks ago by DataFanatic100
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Comment: A: differential gene expression analysis
... "Yes, typically one simply adds batch and RIN as covariates if they seem relevant. " Do you mean that you can add covariates into the model matrix e.g. design<-model.matrix(~group+batch+RIN) Thanks! ...
written 5 weeks ago by DataFanatic100
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differential gene expression analysis
... I'm trying to do differential gene expression analysis (RNA-Seq data) using Limma and EdgeR How can I adjust my count matrix for technical confounders(RIN, batch)? a. Is it possible to adjust for confounders within Limma? b. Can I adjust the count matrix for covariates using linear regression and ...
confounders edger limma rna-seq regression written 5 weeks ago by DataFanatic100
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missing a sample and individual attributes in GTEX Adipose- Subcutaneous(v7)
... I'm working with GTEx Adipose- Subcutaneous(v7) and have several missing sample and individual attributes in the GTEx Subcutaneous Adipose, specifically: Adipose - Subcutaneous=294 samples in the genotype file Adipose - Subcutaneous=294 samples in the expression values When subsetting the indi ...
adipose rna-seq gtex written 4 months ago by DataFanatic100
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Comment: C: Working with GTEX dataset
... Did you ever figure the solution to this? I'm working with GTEx Adipose(v7) - Subcutaneous and have several missing a sample and individual attributes: Adipose - Subcutaneous=294 samples in the genotypes Adipose - Subcutaneous=294 samples in the expression values Adipose - Subcutaneous=138 samples ...
written 4 months ago by DataFanatic100
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Answer: A: remove lowly expressed genes by selecting genes that had FPKM > 0
... Using genefilter library(genefilter) f1<- kOverA(265, 0) ffun <- filterfun(f1) wh1 <- genefilter(exprs, ffun) sum(wh1) exprs.filt<-exprs[wh1,] or exprs.filt.2<-exprs[rowSums(exprs>0)>=265,] To confirm that both methods keep the same genes table(rownames(exprs.filt)==rownames ...
written 4 months ago by DataFanatic100
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remove lowly expressed genes by selecting genes that had FPKM > 0
... Hi, I have to remove lowly expressed genes by selecting genes that had FPKM > 0 in at least 90% of individuals. How can I do this in R? Also In the following expression, I'm confused what the last part, **>= 294** is filtering. table(rowSums(exprs>0)>=294) Thanks! ...
filter rna-seq written 4 months ago by DataFanatic100
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number of individuals in each genotype group for a particular SNP
... I have genotype plink files for 299 individuals and I'm interested in finding the number of individuals in each genotype group for a particular SNP. e.g: SNP1234--> GG n=?; GAn=?; AAn=?. Thanks! ...
plink snp written 4 months ago by DataFanatic100 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: Subsetting individuals with Plink. Error: Line 1 of --keep file has fewer tokens
... Thanks, This fixed my problem. ...
written 4 months ago by DataFanatic100

Latest awards to DataFanatic

Supporter 8 months ago, voted at least 25 times.
Popular Question 13 months ago, created a question with more than 1,000 views. For merging two bigwig files

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