User: peter robinson

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Posts by peter robinson

<prev • 30 results • page 3 of 3 • next >
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Comment: C: RMA vs VSN
... On Monday 21 June 2004 21:08, Roger Vallejo wrote: > This must be of interest for those preprocessing data from affymetrix > chips. We have compared RMA vs VSN performing an lme-ANOVA. If you are > wondering what to use RMA or VSN? or what are the potential pitfalls or > benefits from us ...
written 15.5 years ago by peter robinson300
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affyRNADeg
... Dear List members, I was wondering if someone could tell me how to label individual curves in the AffyRNADeg plots? Thanks Peter ...
written 15.5 years ago by peter robinson300
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Answer: A: Statistics::R
... Thanks. I have been making a summary HTML page for QC for all Chips in an experiment by extracting salient features from the RPT files with Perl and displaying them as a table and creating images such as RNAdeg plots in R. This page is linked to other pages with expression data/differentially regula ...
written 15.6 years ago by peter robinson300
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Statistics::R
... Dear Bioconductors, I have been experimenting with various ways of scripting the analysis of affymetrix data with bioconductor and perl. I would like to more or less automatically create a set of HTML pages with summary data and images of the chips, RNA degradation plots etc. I would like to use a ...
written 15.6 years ago by peter robinson300
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MOE430 A and B
... Dear List members, I would like to use the affy package to analyze data from MOE430A and -B chips. I tried to read in data from both types of chips at once using data <- ReadAffy(widget=T) and then reading in 3 MOE430A and 3 MOE430B CEL files. I got the error message: "Cel file does not seem to ...
moe430a moe430b cdf affy written 15.8 years ago by peter robinson300 • updated 15.8 years ago by Aedin Culhane310
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Answer: A: RNA digestion plots
... I am looking for help in the interpretation of RNA digestion plots. If I have understood the recent discussions, then one expects to see a trend from 3' to 5' in average probe intensity. I am comparing two sets of experiments done in two different labs. Both were done with mgu74av2 chips. One set i ...
written 16.1 years ago by peter robinson300
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diff (Beginner's question)
... Dear all, I have analyzed one data with (8 arrays of 4 wildtype and 4 ko) set basically according to the methods outlined in the End2Endlab vignette. The analysis includes a function: scores <- esApply(eset,1,function(x) { tmp <- t.test(x[index2],x[index1],var.equal=T) c(mean(tmp$estimate),- ...
written 16.1 years ago by peter robinson300 • updated 16.1 years ago by Adaikalavan RAMASAMY80
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[bioC] complete analysis > session from start to finish
... > Hi -- > > On Wed, 19 Nov 2003, Warnes, Gregory R wrote: > > 2) None of the vignettes that I've looked at show a complete analysis > > session from start to finish. Take a look at End2EndLab, which describes analysis of affymetrix data from start to finish with some of the man ...
written 16.1 years ago by peter robinson300 • updated 16.1 years ago by rgentleman5.5k
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Answer: A: affy troubles
... => Ken, thanks. My main difficulty, which presumably comes from lack of sufficient experience with bioconductor, is that the object ex appeared to be different from the matrix object "golub", which is a matrix instance used in the vignette for the multtest package. This instance also has the attr ...
written 16.1 years ago by peter robinson300
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affy troubles
... Dear Bioconductors, I would like to use the affy and multtest packages to extract a list of differentially expressed genes from a set of 8 experiments, in which 4 are wildtype and 4 are knockouts. I have worked through several of the affymetric vignettes and the mult test vignette, which are all ve ...
probe multtest affy written 16.1 years ago by peter robinson300

Latest awards to peter robinson

Popular Question 10.4 years ago, created a question with more than 1,000 views. For Filtering by fold change
Popular Question 10.4 years ago, created a question with more than 1,000 views. For Cannot load preprocessCore.so
Popular Question 10.4 years ago, created a question with more than 1,000 views. For Affymetrix probeset ids to gene symbols
Popular Question 10.4 years ago, created a question with more than 1,000 views. For How to go from affymetrix to Ensembl transcript IDs
Popular Question 10.4 years ago, created a question with more than 1,000 views. For Differential expression in time series
Popular Question 10.4 years ago, created a question with more than 1,000 views. For Mapping Agilent Probes

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