User: elliot harrison

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Posts by elliot harrison

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Updated affy package? ReadAffy/ AffyBatch has change and breaks my pipeline!
... I'm not sure if this will work but I'm trying to tag an answer onto an old question from a year ago, will copying the subject line from that query achieve that? The original query can be found here: http://comments.gmane.org/gmane.science.biology.informatics.conductor/ 39289 I did not see a resol ...
cdf affy written 5.1 years ago by elliot harrison230
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RSD Log Ratio Data
... Hi, I need to calculate some data regarding the variance of probes across samples. Typically we have expressed this as the relative standard deviation before. However, I have only done this for 1 colour data previously and the dataset I am working with is 2 colour common reference data. When I repe ...
written 7.1 years ago by elliot harrison230
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Comment: C: paired sample LIMMA
... Hi Achilleas, Thanks for that yes that is what I was expecting to see. Thank you. Can you shed any light on how I should define the contrast matrix? Thanks E From: Achilleas Pitsillides [mailto:anp4r@virginia.edu] Sent: 26 May 2011 14:55 To: elliott harrison Cc: bioconductor@r-project.org Subjec ...
written 7.2 years ago by elliot harrison230
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paired sample LIMMA
... Hi BioC, I have a question regarding the output of a LIMMA. I have 2 colour data with a constant reference. Some googling lead me to some references that as I have a constant dereference I can set up a paired comparison as in the limma example. I have the following targets file > targets ...
limma cycle written 7.2 years ago by elliot harrison230 • updated 7.2 years ago by Achilleas Pitsillides170
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R/Bioconductor validation
... Hi BioC, We are undergoing a process of validating our systems and software. I was wondering has anyone gone through the process of validation with R and if so could you point me to any resources that may help show how this should be done? Thanks Elliott ...
process written 7.8 years ago by elliot harrison230 • updated 7.8 years ago by Martin Morgan ♦♦ 22k
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Answer: A: ArrayQualityMetrics: Problem with labels in plots
... HI Audrey, Thanks for getting back to me. rg is an rglist with 4 channels > class(rg) [1] "RGList" attr(,"package") [1] "limma" > summary(rg) Length Class Mode G 1133568 -none- numeric Gb 1133568 -none- numeric R 1133568 -none- numeric Rb 11335 ...
written 8.8 years ago by elliot harrison230
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ArrayQualityMetrics: Problem with labels in plots
... Hi BioC, I was suffering with this problem so followed the conversation which led to a conclusion last week. I have installed version 2.4.1 this morning. I like to run the arrayQualityMetrics on both the raw and Normalised data. The normalised data runs fine and I'm happy to report the labelling is ...
annotation arrayqualitymetrics written 8.8 years ago by elliot harrison230
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Determining which comparisons show significant difference Multi-class SAM
... Hi BioC, I've had a good hunt through the documentation but can't find a solution to this. Is it possible to determine between which classes a probes has a delta value above the threshold and perhaps output that along with the significant probes? For example Say the following design cl <- c( ...
probe written 8.9 years ago by elliot harrison230
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Answer: A: Help with loop logic
... Hi Jim, Thanks that is great stopped me going round the houses to achieve this. Elliott Message: 12 Date: Fri, 24 Jul 2009 11:32:55 -0400 From: "James W. MacDonald" Subject: Re: [BioC] Help with loop logic To: elliott harrison Cc: bioconductor@stat.math.ethz.ch Message-ID: <4A6 ...
written 9.1 years ago by elliot harrison230
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Help with loop logic
... Hi BioC, I'm working on a code to create a contrast matrix from the values listed against array file in the targets file. I can parse unique values from the input file ok but then I want to iterate over them to make the comparisons and matrix Group1-group2,group1-group3,group2-group3 I ...
written 9.1 years ago by elliot harrison230

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