User: Asma rabe

gravatar for Asma rabe
Asma rabe290
Reputation:
290
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Trusted
Location:
Japan
Last seen:
1 year, 5 months ago
Joined:
8 years, 1 month ago
Email:
a********@gmail.com

Posts by Asma rabe

<prev • 99 results • page 1 of 10 • next >
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Comment: C: bumphunter of multi covariates
... Thank you James. The reference is considered as the element with the lowest number or letter with lowest alphabetical order (first element in levels of the factor object ) not on the order of data in the factor object Thanks for the advice.   ...
written 2.9 years ago by Asma rabe290
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Answer: A: bumphunter of multi covariates
... Thank you James. I have two questions 1)If i have more than two conditions, it will be (Drug1_disease - Drug1_control) - (Drug2_disease - Drug2_control)-(Drug3_disease - Drug3_control) - (Drug4_disease - Drug4_control)? 2)#========regarding the original design matrix which have only disease/cont ...
written 2.9 years ago by Asma rabe290
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Comment: C: bumphunter of multi covariates
... Thank you James . Using the coefficient which is value column in the table of bump hunter output, the sign can tell if the region is hypo/hyper methylated in the disease relative to normal. How to infer which region of disease is hypomethylated in one condition relative to other condition? would y ...
written 2.9 years ago by Asma rabe290
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bumphunter of multi covariates
... Hi, I have used bump hunter function for two populations (control and disease represented by status column) using the following formula designMatrix <- model.matrix(~ status) For each of control and disease populations,within each population, I have subpouations treated with different drugs I ...
bumphunter written 2.9 years ago by Asma rabe290
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Comment: C: Genomic features for genomic positions
... Thank you very much. Great package! I could annotate the regions using locateVariants The output has many redundancies. I used ?unique  to remove redundant columns from GRanges object.   ...
written 2.9 years ago by Asma rabe290
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Genomic features for genomic positions
... I have a list of regions identified as differentially methylated regions using bump hunter in minfi package with the format chr  start  end …. chr1 chr2 chr3 …. I want to identify genomic features of these positions (5' UTR, exon, gene body or 3' UTR) I fought of using findOverlaps and conver ...
genomicfeatures written 2.9 years ago by Asma rabe290 • updated 2.9 years ago by Vince Schulz60
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Methylation and gene expression
... Hi, I have methylation data and genes expression data with different samples size. For example(10 methylation samples,15 gene expression samples). I identified DMRs using bump hunter in minfi package. I want to integrate gene expression and methylation data using DMRs identified using bump hunter. ...
geneexpression methylation written 2.9 years ago by Asma rabe290
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Comment: C: Positions to genes in minfi
... Hi James, nearest helped me to find the nearest gene to the DMR. nearest(x, subject, select ="all") returns all overlapping regions which are mostly redundant transcript, since i am interested in unique gene names I used nearest(x, subject) #arbitrary is the default. How to ensure that a single ...
written 2.9 years ago by Asma rabe290
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Answer: A: Positions to genes in minfi
... Hi James, nearest helped me to find the nearest gene to the DMR. nearest(x, subject, select ="all") returns all overlapping regions which are mostly redundant transcript, since i am interested in unique gene names I used nearest(x, subject) #arbitrary is the default. How to ensure that a single ...
written 2.9 years ago by Asma rabe290
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Answer: A: Error when installing ReportingTools
... Hi Martin, Thank you very much. The error was due to that installing RcppArmadillo package requires gcc version > gcc4.6. It works when i installed gcc4.8. Again. Thank you! ...
written 3.0 years ago by Asma rabe290

Latest awards to Asma rabe

Popular Question 17 months ago, created a question with more than 1,000 views. For RPKM and FPKM
Popular Question 17 months ago, created a question with more than 1,000 views. For EdgeR-tophat
Popular Question 2.9 years ago, created a question with more than 1,000 views. For RPKM and FPKM
Popular Question 2.9 years ago, created a question with more than 1,000 views. For RPKM and FPKM
Popular Question 3.4 years ago, created a question with more than 1,000 views. For GRanges list and reduce function
Scholar 3.4 years ago, created an answer that has been accepted. For A: minfi starting from beta values

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