User: Nathan.Watson-Haigh@csiro.au

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Posts by Nathan.Watson-Haigh@csiro.au

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Agilent duplicate spots and multiple probes per gene
... -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I'm a bit confused/worried about duplicated spots on the Agilent bovine array, in particular how best to handle them in limma as I have technical rep dye-swaps. > #Get all non-control spots: > genes.idx <- which(RG$genes$ControlType == 0) > ...
limma written 10.4 years ago by Nathan.Watson-Haigh@csiro.au210 • updated 10.4 years ago by Peder Worning100
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limma and technical rep dye-swaps
... -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I have an experiment where samples have 1 of 3 phenotype: H, P and S. All pairwise comparisons need to be made, but the P vs H is the most important. As a result we have the following Agilent 2-colour hybridisations in a loop design (there are 4 biologi ...
affy limma written 10.4 years ago by Nathan.Watson-Haigh@csiro.au210
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Agilent 2 colour spike-in controls
... A quick question and hopefully a quick answer in reply.... I have data from Agilent bovine chips. Are the spike-in probe replicates (of which there are 32 on each chip) supposed to be highly replicable on an MA plot? Some of my chips show good reproducibility of the spike- in's on MA plots, but oth ...
written 10.4 years ago by Nathan.Watson-Haigh@csiro.au210 • updated 10.4 years ago by Naomi Altman6.0k
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self-self hybridisations to estimate dye-bias
... Hi all, I'm new to 2-colour arrays and I've been reading with interest a few papers about dye-bias: Dobbin, K., Shih, J.H. & Simon, R., 2003. Statistical design of reverse dye microarrays. Bioinformatics, 19(7), 803-810. Dombkowski, A.A. et al., 2004. Gene-specific dye bias in microarray refe ...
microarray limma written 10.5 years ago by Nathan.Watson-Haigh@csiro.au210
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Experimental Design Question(s)
... I'm trying to understand and analyse a microarray experiment performed by someone else, and I've been reading about experimental design in some books and have a few questions. The experiment involves groups of animals assigned to one of 3 time points (measured as the number of days since treatment) ...
microarray limma written 11.0 years ago by Nathan.Watson-Haigh@csiro.au210
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Answer: A: Error in RCurl and GEOquery installation
... You may also need to install the curl-devel package (which I think has curl-config). In addition, once R can fine curl-config, you may encounter a problem which I had, which seemed to be that Rcurl 0.9-3 mistook my system for a 64bit OS rather than a 32Bit OS. As a result, I was forced to install an ...
written 11.2 years ago by Nathan.Watson-Haigh@csiro.au210
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Answer: A: Experimental Design, Model Matrix and Contrasts
... If I do as you say, I have three factors with two levels each: Treatment - "C" and "T" Gestation - "d60" and "d67" Contamination - 0 and 1 I set up the design matrix as follows: TG<-paste(pData(eSet)$Treatment, pData(eSet)$Gestation, pData(eSet)$Muscle_Contamination, sep=".") TG<-factor(TG,le ...
written 11.2 years ago by Nathan.Watson-Haigh@csiro.au210
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Answer: A: How to objectively evaluate chip quality?
... Hi Mark, Unfortunately, I have no experience of the Exon ST arrays, so can't give any specific help...sorry. Nathan -----Original Message----- From: Mark Cowley [mailto:m.cowley0@gmail.com] Sent: Monday, 21 July 2008 8:44 AM To: Watson-Haigh, Nathan (LI, Rock. Rendel) Cc: bioconductor list Subjec ...
written 11.2 years ago by Nathan.Watson-Haigh@csiro.au210
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Affy array layout
... I want to generate some quality control plots for Affymetrix arrays (initially bovine and Arabidopsis). I'd like to know more about the layout of probes on the array. For instance, when I get the pm and mm probes separately, the number returned is different from that returned by intensity(), why is ...
written 11.2 years ago by Nathan.Watson-Haigh@csiro.au210 • updated 11.2 years ago by Kasper Daniel Hansen6.4k
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Experimental Design, Model Matrix and Contrasts
... I'm getting myself confused with setting up these things for a limma analysis. Please stop me and correct me if I'm wrong with any of this! I have two factors each with two levels: Treatment - "C" and "T" Gestation - "d60" and "d67" I setup up my model and design matrix as follows: TG<-paste(p ...
written 11.2 years ago by Nathan.Watson-Haigh@csiro.au210

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