User: Scott Robinson

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Posts by Scott Robinson

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Comment: C: Using custom CDF with 'make.cdf.env'
... Ah! Sorry, reading that reply I instantly saw the problem ? I forgot to change the probe set ID for the individual rows. Thanks very much James From: James W. MacDonald [mailto:jmacdon@uw.edu] Sent: 27 August 2014 16:52 To: Scott Robinson Cc: bioconductor at r-project.org Subject: Re: Using custo ...
written 4.3 years ago by Scott Robinson130
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Comment: C: Using custom CDF with 'make.cdf.env'
... Hi James, Thanks for the quick response. If you open the new CDF in a text editor like notepad++ and use a find & count function you will find there are only 12,380 matches to the text string ?[Unit?. This string matches both the ?Unit###? section and the ?Unit###_Block#? sections for each prob ...
written 4.3 years ago by Scott Robinson130
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Answer: A: Using custom CDF with 'make.cdf.env'
... Dear All, Since it exceeds 1MB, here is a link to the old ("miRNA-1_0.CDF") and new ("newmir1.cdf") CDFs, test script and example CEL file: http://www.files.com/set/53fdeb0aa2176 Thanks, Scott ________________________________________ From: Scott Robinson [guest] [guest@bioconductor.org] Sent: 27 ...
written 4.3 years ago by Scott Robinson130
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Can I input ordinal variables into a model in Limma?
... Dear Gordon, I implemented this and am wondering how you interpret logFC from topTable with regards the linear trend? I have tried replicating it, but no joy. Thanks, Scott PS code below: design <- model.matrix(~copd + asthma + smoking + sex) > design (Intercept) copd.L cop ...
microarray limma written 4.8 years ago by Scott Robinson130 • updated 4.8 years ago by Gordon Smyth35k
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Comment: C: affyPLM crashing R
... Apologies, have found the mistake in my code - I had a number of affybatch objects floating around my script and had input the one with the NAs into fitPLM. Strange that it made R crash rather than just give me an error saying that it couldn't work with missing values. I am now getting the error me ...
written 5.0 years ago by Scott Robinson130
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Comment: C: affyPLM crashing R
... Never mind that last e-mail, it will be small enough zipped. Just wasn't thinking. I will make a small example tomorrow and reply again. Many thanks, Scott -----Original Message----- From: Wolfgang Huber [mailto:whuber@embl.de] Sent: 05 December 2013 14:41 To: Scott Robinson [guest] Cc: Bioconduc ...
written 5.0 years ago by Scott Robinson130
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Comment: C: affyPLM crashing R
... Dear Wolfgang, I would have provided a reproducible example but even one of the CEL files alone is above my attachment size limit. Perhaps I could send you a short version of my R script and my Java program and you could try it on some CEL files of your own? Or maybe I could try sending a reproduci ...
written 5.0 years ago by Scott Robinson130
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How does one deal with spatial effects detected on single channel microarrays?
... Dear All, Sorry about the delay, I was given other priorities and am just getting back to this. I read the tutorial and the paper on that harshlight package and it looks good. Can anyone think of a reason that it only has 19 citations on pubmed despite being published back in 2005? Is it simply th ...
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Comment: C: How does one deal with spatial effects detected on single channel microarrays?
... Dear Christian, Brilliant, thanks very much. I have just one last query: if I were to have a more detrimental spatial effect do you (or anyone) know what BioC package (if any exists) would be appropriate for spatial normalization of single-channel Affy chips? Or is it simply a case of removing that ...
written 5.3 years ago by Scott Robinson130
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Comment: C: How does one deal with spatial effects detected on single channel microarrays?
... Dear Christian, Thanks very much for the help. I especially like the "crop circles" artefact. So is the idea that if you have a small spatial artefact it's probably going to affect only a small number of the probes in each probe set and therefore not affect the summarised values much? Do you only ...
written 5.3 years ago by Scott Robinson130

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