User: Johnstone, Alice

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Posts by Johnstone, Alice

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average difference and global scaling for normalizing affymetrix expression data?
... Hello, I have been asked to look at data from the GEO to make a comparison with current microarray data. The GEO data is from an Affymetrix Murine Genome U74 Version 2 Array experiment, from 2003 and the description says that the data is the "average difference" with "global scaling" applied. Thi ...
microarray limma written 9.2 years ago by Johnstone, Alice410 • updated 9.2 years ago by Wolfgang Huber13k
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Comment: C: row clustering in heatmap.2
... Ahh thanks for your reply Mark, I had atempted this yesterday using row means of the treatment.. but was of course still getting a mix of up and down as I wasn't accounting for the expression level in the control. Looks great now. Cheers Alice -----Original Message----- From: Mark Cowley [mailto:m. ...
written 11.3 years ago by Johnstone, Alice410
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row clustering in heatmap.2
... Hi Im having a hard time trying to understand the clustering functions used with heatmap.2. I have expression data, treatment vs control for which I have created a heatmap for (default arguments). But I want to reorder the rows so that the row with the highest expression in my treatment is at the ...
go clustering written 11.3 years ago by Johnstone, Alice410 • updated 11.3 years ago by Mark Cowley400
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GSEA GeneSetCollection for GO info from Illumina annotation package
... Hi, I am having some trouble creating a geneset collection for GO data from the Illumina annotation package illuminaRatBCv1. I can create the KEGG set fine as shown below, but when I try the same for GO info I get the error below: > illumina.rat.kegg<-GeneSetCollection(idType=AnnotationIdent ...
annotation go written 11.4 years ago by Johnstone, Alice410
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Comment: C: GSEA GeneSetCollection
... Thanks Martin! The code worked and there were no problems importing the file. Regards Alice -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: Saturday, 7 June 2008 1:54 a.m. To: Johnstone, Alice Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] GSEA GeneSetCo ...
written 11.4 years ago by Johnstone, Alice410
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GSEA GeneSetCollection
... Hi I have been using the GSEA java version to look at my microarray results. I ran into a problem as my samples are from rat. I therefore want to create my own gene sets based on KEGG and GO information in the annotation packages. I have used the command gsc<-GeneSetCollection(Data,setType=KEG ...
go written 11.4 years ago by Johnstone, Alice410 • updated 11.4 years ago by Martin Morgan ♦♦ 23k
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Answer: A: readBeadSummaryData problem- duplicate row name error
... Hi Peter To make sure you are using the correct version of beadarray you should install it with the following command: source("http://bioconductor.org/biocLite.R") biocLite("beadarray") That will avoid the error you are getting with it being built with 2.7.0. as for the duplicate row.names error, ...
written 11.5 years ago by Johnstone, Alice410
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How to remove probes from Illumina data?
... Hello, I have bead-level data from an Illumina expression experiment. I have background corrected and summarised the data, but I need to take the control probes information out of the ExpressionSetIllumina object, or remove them from the beadlevel list. I have tried a few things but they stop me ...
go written 11.6 years ago by Johnstone, Alice410 • updated 11.6 years ago by Matt Ritchie460
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Answer: A: What should happen to control probe information in bead level Illumina analyses?
... Thanks for your reply Simon, Yes the expression level is at the low end of the range so I do not think that this is a hybridisation problem as the original control plots looked fine. I used the VST transformation with a quantile normalisation of the Bead Summary data. My question is whether it is co ...
written 11.6 years ago by Johnstone, Alice410
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What should happen to control probe information in bead level Illumina analyses?
... Hi again! When running through my analysis of bead summary data that I have created from bead level data (background corrected with normexp, and summarised standard) I produced a topTable list which contains probeIDs that are not found in Illumina's reference file. When I checked the controlprobep ...
written 11.6 years ago by Johnstone, Alice410

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Popular Question 9.2 years ago, created a question with more than 1,000 views. For read.phenoData vs read.AnnotatedDataFrame

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