User: Frocha

gravatar for Frocha
Frocha10
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10
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New User
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4 months, 1 week ago
Joined:
1 year, 9 months ago
Email:
n****@ucmail.uc.edu

Posts by Frocha

<prev • 28 results • page 1 of 3 • next >
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How to read in PacBio .bam.pbi file
... I want to read a PacBio .bam.pbi file (the index file for a PacBio bam file) into R. How can I read it? Thanks! ...
pacbio pbi written 4 months ago by Frocha10
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Comment: C: Should I use legacy functions in ShortRead package?
... Thanks a lot! ...
written 6 months ago by Frocha10
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Comment: C: Should I use legacy functions in ShortRead package?
... So sread() is not a legacy function? ...
written 6 months ago by Frocha10
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Should I use legacy functions in ShortRead package?
... I am developing an R package and it depends on ShortRead package. In particular, I am using sread() function in the ShortRead package. I noticed that the sread() function is one of the "(Legacy) Accessors for ShortRead classes“ (ShortRead manual). What does "legacy" mean? Can I use the sread() funct ...
shortread written 6 months ago by Frocha10 • updated 6 months ago by Martin Morgan ♦♦ 22k
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How to get disease free survival information from TCGA using TCGAbiolinks?
... I wish to get disease free survival information for all patients with a particular tumor from TCGA. I can use TCGAbiolinks to extract the clinical data. But how can I extract the disease free survival information? Thanks! ...
tcga tcgabiolinks written 6 months 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
... 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 7 months 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 7 months 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 7 months 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 7 months 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 7 months ago by Frocha10 • updated 7 months ago by Gordon Smyth35k

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