User: Matthew Hobbs

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m*****@gimr.garvan.unsw.edu.au

Posts by Matthew Hobbs

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RMA publications
... Can anyone direct me to some research publications which make use of both quantile normalization and RMA? Thanks -- ---------------------------------------------------------------------- Matthew Hobbs Garvan Institute of Medical Research 384 Victoria St Ph : (02) 9295 8327 Darlinghur ...
normalization written 16.4 years ago by Matthew Hobbs80 • updated 16.4 years ago by Rafael A. Irizarry2.3k
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Answer: A: com.braju.sma
... In affy the plotLocation function allows me to display probe locations on a celfile image, but is it possible to go in the other direction i.e. derive the identities of probes related to a particular area on an image (perhaps specified interactively by pointing and clicking). Thanks -- ----------- ...
written 16.5 years ago by Matthew Hobbs80
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Comment: C: Volcano plots
... I too have been wondering about the usefulness of the volcano plot and so was interested in this thread. But (excuse my slowness) what's the answer to the original question about whether they can be used to help detect differentially expressed genes? Matthew > recently I was asked about volc ...
written 16.5 years ago by Matthew Hobbs80
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Comment: C: MGU74A and MGU74Av2
... Thanks to everyone for the helpful responses. On Sat, 21 Jun 2003 06:10 am, Ben Bolstad wrote: > You have several options. I will probably look into both. > 1. treat the MGU74a and MGU74av2 seperately, then try to figure out a > way to combine them. > 2. Look at only the common probe ...
written 16.5 years ago by Matthew Hobbs80
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MGU74A and MGU74Av2
... Hi, I have some cel files from experiments using the Affy MGU74A chip and some from experiments using the MGU74Av2 chip. Am I right in thinking that MGU74A and MGU74Av2 are actually the same chip described differently (because some probesets were originally designed wrongly)? I wish to treat al ...
mgu74a mgu74av2 cdf affy written 16.5 years ago by Matthew Hobbs80 • updated 16.5 years ago by Susan G. Hilsenbeck10
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using geneplotter with my own data
... Hi, I am relatively new to R and BioConductor and despite looking at the help documents and vignettes am struggling with lots of things. At the moment I am trying to do something useful with the cPlot function from geneplotter. This runs OK when I follow the examples but these use data that I'm n ...
geneplotter written 16.5 years ago by Matthew Hobbs80 • updated 16.5 years ago by Jeff Gentry3.9k
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Answer: A: affy normalization
... Whoops! I asked a dumb question. I see now normalize.quantiles can use as an argument a matrix instead of an AffyBatch object. Sorry about the unneccessary posting. Hi, I have been wondering about how to do quantile normalization of affy data for which probe-level data is not available. I foun ...
written 16.6 years ago by Matthew Hobbs80
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Answer: A: affy normalization
... Hi, I have been wondering about how to do quantile normalization of affy data for which probe-level data is not available. I found an answer in the mailing list archive (see below) but I'm afraid I can't find the vignette referred to nor can I find any information about whatever function is wrapp ...
written 16.6 years ago by Matthew Hobbs80

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