User: Hugh Shanahan

gravatar for Hugh Shanahan
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h***@cs.rhul.ac.uk

Posts by Hugh Shanahan

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SRAmetadb Bioconductor package; study record count low for 2013
... Thanks Jack ! Sent from my phone so apologies for my brevity and frequent typos. -------- Original message -------- From: Jack Zhu Date: 17/06/2014 20:31 (GMT+00:00) To: Sean Davis ,"Shanahan, Hugh" ,bioconductor@r-project.org,Jamie.Al- Nasir.2012@live.rhul.ac.uk Subject: Re: [BioC] SRAmetadb ...
sradb written 3.4 years ago by Hugh Shanahan50
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query on variance parameters for RMA
... Hi, we would like to compute the parameters (i.e, the other parameters that are computed via the median polish algorithm) that are computed in the final summarisation step in RMA. In particular, we'd like to determine the parameter alpha_i that tells us how the estimate for the expression vari ...
probe written 4.8 years ago by Hugh Shanahan50 • updated 4.8 years ago by James W. MacDonald45k
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Comment: C: Error message (probably) from AffyBatch.R when using a modified CDF
... Okay - the problem is fixed now. The trouble was that the filter was occasionally leaving only one probe in the probe set and entry was no longer regarded having the same dimensions as a matrix. Thank you ! Hugh ----- Original Message ----- From: "James W. MacDonald" To: "Hugh Shanahan" Cc: ...
written 4.8 years ago by Hugh Shanahan50
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Error message (probably) from AffyBatch.R when using a modified CDF
... We are writing a new R package to construct CDF's with particular subsets of probes removed. We are building the CDF packages using a modification of makecdfenv. Up until recently, everything has been working fine when we update the CDF library name of an expression set, i.e. > raw <- ReadAffy ...
cdf affy makecdfenv written 4.8 years ago by Hugh Shanahan50 • updated 4.8 years ago by James W. MacDonald45k
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makeProbePackage deprecated in AnnotationDbi ?
... Hi, I've noticed that AnnotationDbi (v 1.2) no longer has makeProbePackage . Has this been replaced by a different function or has it been hived off to a different package ? Many thanks Hugh -- ---------------------------------------------------------------------- -- Hugh Shanahan ...
annotationdbi written 5.1 years ago by Hugh Shanahan50 • updated 5.1 years ago by Martin Morgan ♦♦ 20k

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