User: Claire Wilson

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Claire Wilson280
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Posts by Claire Wilson

<prev • 28 results • page 1 of 3 • next >
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Answer: A: how to select on Present calls in 2 out of 5 chips
... Or alternatively you can use rowSums (assuming x contains your matrix of PMA calls): calls.sum <- rowSums(x=="P") keep <- names(calls.sum[calls.sum>=2]) It's a little faster! claire -- Claire Wilson Bioinformatics Group Paterson Institute for Cancer Research Christie Hospital NHS Trust W ...
written 14.2 years ago by Claire Wilson280
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Answer: A: filtering for present calls
... Hi Josh, Not sure whether anyone has responded to your mail yet, but I think an easier way to do this would be to load your data in, normalise it then calculate detection calls (present/absent calls) and then use these to filter only out those probesets called present.. library(simpleaffy) library ...
written 14.4 years ago by Claire Wilson280
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Detection call for Hu6800
... Hi Christian, This error arises because simpleaffy doesn't know what the alpha1 and alpha2 values are for the Hu6800 chips and you need to supply them with the call to detection.p.val pv17 <- detection.p.val(M17, alpha1=X,alpha2=Y) Hope this helps Claire > -----Original Message----- > ...
hu6800 probe simpleaffy written 14.7 years ago by Claire Wilson280 • updated 14.7 years ago by Christian.Stratowa@vie.boehringer-ingelheim.com270
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Microarray data analysis for experiments using amplifiedRNA
... Dear all, We found similar things when we looked at the standard and small sample (amplification) protocols from Affymetrix (Wilson et al 2004, Biotechniques. 2004 Mar;36(3):498-506). Whilst raw expression levels from unamplified and amplified arrays were not directly comparable, fold-changes were ...
microarray cancer affy written 14.8 years ago by Claire Wilson280
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Answer: A: mas5call select genes
... Hi Katleen, This is the function I use on a matrix of Affymetrix Absent/Present calls (rows are probesets, columns are chips) number.pres <- function(x) { x[x=="P"] <- 1; x[x!=1] <- 0; return(apply(x,1,function(a) { sum(as.integer(a))})) } # Calculate present/a ...
written 14.9 years ago by Claire Wilson280
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error following cluster example
... > Dear Users, > > I am following the example on Lab 5: Cluster analysis (June > 2003) with > my own data. > > I have filtered my expression set as shown on the example and I get > the following > > > sub <- genefilter(X,ffun) > > sum(sub) > [1] 1124 > ...
written 15.1 years ago by Claire Wilson280 • updated 15.1 years ago by rgentleman5.5k
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Answer: A: heatmap genenames
... Hello, Many thanks for your reply, I have tried repeating the clustering done by heatmap using hclust to obtain the row order as follows: d <- dist(mydata) hc.d <- hclust(d) gene.order <- hc.d$order and compared the order to what I see on a heatmap when I do heatmap(mydata) However, i ...
written 15.1 years ago by Claire Wilson280
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heatmap genenames
... Dear all, I have been using the heatmap function to visualise my data and would like to obtain a list of my genes in the same order that they appear in the heatmap. I have looked through the mail archives and tried just creating a dendogram and using order.dendogram but have so far been unsuccessfu ...
written 15.1 years ago by Claire Wilson280 • updated 15.1 years ago by Francois Pepin1.3k
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Answer: A: regarding saving R graphis images directly to directory
... The simpleaffy package has a function screenpng that will allow you to save any images as .png files hope this helps claire > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of SAURIN > Sent: 20 June ...
written 15.5 years ago by Claire Wilson280
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factDesign - another question
... Dear all, I have been working through the factDesign vignette and it appears that the probeset identifiers have been lost from the expression set and also that the expression calls appear to not be in log2 form as indicated in the vignette(code shown below)...thanks for any help, claire > librar ...
factdesign written 15.6 years ago by Claire Wilson280 • updated 15.6 years ago by Denise Scholtens40

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