User: Gundala Viswanath

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Posts by Gundala Viswanath

<prev • 23 results • page 1 of 3 • next >
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Why daisy() in cluster library failed to exclude NA when computing dissimilarity
... Hi, According to daisy function from cluster documentation, it can compute dissimilarity when NA (missing) value(s) is present. http://stat.ethz.ch/R-manual/R-devel/library/cluster/html/daisy.html But why when I tried this code library(cluster) x <- c(1.115,NA,NA,0.971,NA) y <- c(NA,1.006 ...
written 5.9 years ago by Gundala Viswanath230 • updated 5.9 years ago by James W. MacDonald51k
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Comment: C: Dealing with probes with high fold change but PA call 0
... Yes. PA call means present and absent calls. My main questions is actually If a probe have a pa call zero. What is the reasonable expression value we can assign to it? NA or zero. > > I found cases where probe may have a high fold change (>= 5) > > but the Pa call is 0. > > & ...
written 5.9 years ago by Gundala Viswanath230
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Dealing with probes with high fold change but PA call 0
... I have an Affymetrix library which I compute the fold change and PA call for every probe with Bioconductor. I found cases where probe may have a high fold change (>= 5) but the Pa call is 0. My question is, how can we interpret such cases? Should we assign the probe fold change to be 0 or 1? W ...
clustering probe assign written 5.9 years ago by Gundala Viswanath230 • updated 5.9 years ago by Steve Lianoglou12k
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How to deal with Affymetrix probe that map to multiple genes
... Given a (e.g.431765_a_at), I'm trying to find the gene symbol. But some how it gives multiple genes. How can I interpret that properly? This is the example code and output: library(biomaRt) mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") getBM( c("affy_mouse430_2", "mgi_symbol"), ...
go clustering probe convert written 6.2 years ago by Gundala Viswanath230
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Answer: A: How to deal with Affymetrix probe that map to multiple genes
... Given a (e.g.431765_a_at), I'm trying to find the gene symbol. But some how it gives multiple genes. How can I interpret that properly? This is the example code and output: library(biomaRt) mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") getBM( c("affy_mouse430_2", "mgi_symbol"), ...
written 6.2 years ago by Gundala Viswanath230
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Converting Affymetrix (*_at) Mouse Probe ID to HUGO gene symbol
... I have the following list of probes (from Mouse), 1460644_at 1460645_at The longer list can be found here: http://dpaste.com/1371949/plain/ What I want to do is to convert that name with HUGO gene symbol using R. What's the way to do it? I tried this but failed __BEGIN__ library(biomaRt) dat< ...
convert written 6.2 years ago by Gundala Viswanath230
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Answer: A: Converting Affymetrix (*_at) Mouse Probe ID to HUGO gene symbol
... I have the following list of probes (from Mouse), 1460644_at 1460645_at The longer list can be found here: http://dpaste.com/1371949/plain/ What I want to do is to convert that name with HUGO gene symbol using R. What's the way to do it? I tried this but failed __BEGIN__ library(biomaRt) dat< ...
written 6.2 years ago by Gundala Viswanath230
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RMA normalization for Affymetrix CEL Files (Subscript out of bounds error)
... I have an Affymetrix CEL files downloadable here (31.7MB): http://hugefiles.net/4fqnokdo9irv What I want to do is to perform an RMA analysis using affy package. This is the code __BEGIN__ #!/usr/bin/Rscript #install the core bioconductor packages, if not already installed source("http://bioconduc ...
normalization affy written 6.2 years ago by Gundala Viswanath230
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Answer: A: RMA normalization for Affymetrix CEL Files (Subscript out of bounds error)
... I have an Affymetrix CEL files downloadable here (31.7MB): http://hugefiles.net/4fqnokdo9irv What I want to do is to perform an RMA analysis using affy package. This is the code __BEGIN__ #!/usr/bin/Rscript #install the core bioconductor packages, if not already installed source("http://bioconduc ...
written 6.2 years ago by Gundala Viswanath230
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How to use 'ebayes' for small samples?
... I have the following expression data from test and control, each contain two sample. test <- c(3922.89022881,4235.76026274) control <- c(3694.11962861,4369.97835686) I want to compute P-value using , to see if they are differentially expressed, using "ebayes" http://rss.acs.unt.edu/Rdoc/li ...
go written 6.6 years ago by Gundala Viswanath230 • updated 6.6 years ago by James W. MacDonald51k

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