User: Frocha

gravatar for Frocha
Frocha10
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10
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New User
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1 week, 6 days ago
Joined:
1 year, 2 months ago
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n****@ucmail.uc.edu

Posts by Frocha

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Use cpm() in edgeR and voom() in limma to find genes that have low expression in
... You are right. The problem is that the "statmod" package was not installed on my computer, thus the line fit <- eBayes(fit, robust=TRUE) was not executed (I did not notice that). After I installed the "statmod" package, the problem is solved. Thank you very much! ...
written 13 days ago by Frocha10
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Comment: C: Use cpm() in edgeR and voom() in limma to find genes that have low expression in
... I am sorry that I have a new question: there is no p.value information in fit after I run the last line. Is it because that each tumor sample is treated as a single group? If so, how to identify the tumor samples with z-score < -2? ...
written 14 days ago by Frocha10
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Comment: C: Use cpm() in edgeR and voom() in limma to find genes that have low expression in
... Thank you very much! ...
written 15 days ago by Frocha10
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Comment: C: filter genes using cpm() in edgeR and make data normal using voom() in limma
... Sorry for confusing. I wish to get the z-score for each individual tumor for each gene. ...
written 15 days ago by Frocha10
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Comment: C: filter genes using cpm() in edgeR and make data normal using voom() in limma
... Thanks! One question: should we put the design<-model.matrix(~Tumor) line at the beginning? In fact, the goal is not to do differentially expressed gene analysis. The goal is to calculate z-scores for the tumor sample so that we can divide the tumor samples into two groups: those with z-score & ...
written 16 days ago by Frocha10 • updated 15 days ago by Gordon Smyth32k
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Comment: C: filter genes using cpm() in edgeR and make data normal using voom() in limma
... Thanks, Gordon. I wish to identify the tumor samples with low gene expression (compared to normal samples), and then try to see whether the corresponding patients have survival rates that are different from the survival rates of other patients. My question then is: how to best compute the z-scores ...
written 16 days ago by Frocha10
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Use cpm() in edgeR and voom() in limma to find genes that have low expression in individual tumors
... I have RNA-Seq count data for two groups of samples (normal vs tumor). For a specific gene, I wish to find the tumor samples that have low gene expression (compared to the samples in the normal group). The "low" expression means the (possibly transformed) log(cpm) has a z-score < -2, where the z- ...
limma edger gene filtering written 16 days ago by Frocha10 • updated 15 days ago by Gordon Smyth32k
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Comment: C: reduce function in GenomicRanges
... Thank you very much! ...
written 7 months ago by Frocha10
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Comment: C: reduce function in GenomicRanges
... Thank you very much! However, I wish to have a function which allows min.gapwidth option. Is there a way to do so? ...
written 7 months ago by Frocha10
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Comment: C: reduce function in GenomicRanges
... Here is an example: > seqinfo <- Seqinfo("chr1", + seqlengths=100, + isCircular=TRUE) > > gr=GRanges("chr1", IRanges(c(5, 95), c(10, 101)), + strand="*",seqinfo=seqinfo) > > reduce(gr,min.gapwidth=10) GRanges object with 2 ranges and 0 metadata columns:       seqnames    ranges st ...
written 7 months ago by Frocha10

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