User: Joseph Shaw

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Joseph Shaw100
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Posts by Joseph Shaw

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Identifying Processes as Upregulated or Downregulated
... Hi Jim, Thanks so much for clearing that up for me! Joseph On Tue, Feb 11, 2014 at 9:04 PM, James W. MacDonald wrote: > Hi Joseph, > > The flaw in your reasoning is here: > > > "Let's assume that the process represented by GO_A is such that it > cannot be simultaneously upre ...
written 5.2 years ago by Joseph Shaw100
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Comment: C: Identifying Processes as Upregulated or Downregulated
... Hi Jim, Thanks for your reply. My worry, originally, was that that failure to differentiate between upregulated and downregulated processes would lead to spurious results. Let's create another scenario. Assume we have a group of genes identified as upregulated and another group of genes identifie ...
written 5.2 years ago by Joseph Shaw100
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Identifying Processes as Upregulated or Downregulated
... Hi all, I am in the process of performing some ontological analysis with GOstats. Given that GOstats doesn't require any information on relative increases or decreases in expression for its hypergeometric testing procedure, am I correct in assuming that it does not differentiate between upregulated ...
process gostats written 5.2 years ago by Joseph Shaw100 • updated 5.2 years ago by James W. MacDonald49k
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Comment: C: Gene Ontology Annotations from Gene Names
... Hi all, Thank you so much. Your assistance has been invaluable! Joseph On Mon, Feb 10, 2014 at 7:37 PM, Marc Carlson wrote: > Hi Joseph, > > Here is a newer tarball, build with all release packages so that it should > be able to install properly for you without modification. > > ...
written 5.2 years ago by Joseph Shaw100
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Comment: C: Gene Ontology Annotations from Gene Names
... Hi Jim, > You can check to see if it is a viable option by just giving it a shot. I have attempted to call the makeOrgPackageFromNCBI() as described in your previous mail (having provided my details for the author and maintainer arguments); however, the function call doesn't fully complete. In ...
written 5.2 years ago by Joseph Shaw100
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Comment: C: Design/Contrast Matrix for Two Channel Microarray
... Hi Gordon, Thanks for your response - I believe it has cleared everything up. So, for example, for experimental design (d), the simple saturated direct design, we have the design matrix (1 0; 0 1; -1, -1). The first coefficient represents B-A, hence the first row (1 0); the second coefficient rep ...
written 5.2 years ago by Joseph Shaw100
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Comment: C: Gene Ontology Annotations from Gene Names
... Hi Jim, Thanks for your reply! The organism is Campylobacter jejuni (strain: NCTC11168). How can I check if this is a viable option? According to the reference manual for AnnotationForge, the makeOrgPackageFromNCBI() function makes an organism package from annotations available from NCBI, but, ac ...
written 5.2 years ago by Joseph Shaw100
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Comment: C: Design/Contrast for Two-Channel Experimental Setup
... Dear Gordon, > > It is probe-specific, as I said before. No one claimed it was "observation > specific". > My apologies - I didn't mean to imply that anybody had claimed the above. I was just hoping to eliminate some ambiguities that I had held. > > Well, first off, your code n ...
written 5.3 years ago by Joseph Shaw100
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Comment: C: Design/Contrast for Two-Channel Experimental Setup
... Dear Gordon, Thank you very much for your response! I have two brief follow-on questions pertaining to your previous mail. On Sun, Jan 5, 2014 at 10:39 PM, Gordon K Smyth wrote: > >> Date: Sat, 4 Jan 2014 19:58:32 +0000 >> From: Joseph Shaw >> To: Ryan >> Cc: biocond ...
written 5.3 years ago by Joseph Shaw100
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Comment: C: Design/Contrast for Two-Channel Experimental Setup
... Hi Ryan, Thanks for your reply! It was my belief that the experimental setup would imply that the dye effect would be confounded with the biological effect - thanks for clarifying that this is indeed the case. However, I'm still slightly confused about the dye effect term; specifically, shouldn't ...
written 5.3 years ago by Joseph Shaw100

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