User: Mark Cowley

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Mark Cowley910
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Posts by Mark Cowley

<prev • 91 results • page 1 of 10 • next >
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Answer: A: Draft support for HTA 2.0 with oligo
... thanks Benilton! On 09/02/2014, at 8:47 AM, Benilton Carvalho wrote: > Hello, > > given the several requests I got re: supporting HTA 2.0 chips when using > oligo, I'm posting this message to bioc (rather than bioc-devel). > > I'll add support for HTA on our next release. A dra ...
written 3.8 years ago by Mark Cowley910
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Comment: C: Affymetrix HTA 2 array analysis
... Hi Vincent & Benilton, Myself and Philip de Groot have independently tried to create the pd.hta.2.0.db overnight with the same error (though different to your error) on both R 2.15.2 on OSX and R 3.0.0 on linux. I probably should have kept this on-list, so i'm CC'ing the relevant parties here. B ...
written 4.2 years ago by Mark Cowley910
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Affymetrix HTA 2 array analysis
... Hi Steven, Did you manage to create a pd.hta.2.0 package? kind regards, Mark On 20/04/2013, at 7:23 AM, Steven McKinney wrote: > Hi all, > > Has anyone developed bioconductor/R analysis tools for the > Affymetrix Human Transcriptome Array HTA_2_0 ? > > Any information on proces ...
cancer breast written 4.2 years ago by Mark Cowley910 • updated 4.2 years ago by Vincent J. Carey, Jr.6.2k
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Comment: C: pd.hugene.2.0.st missing normgene->exon mappings
... Hi Benilton, That sounds like a great solution. I hope it's not too much work! Mark Sent from my iPhone On 20/07/2013, at 9:25 AM, "Benilton Carvalho" wrote: > Hi Mark et. al., > > On the initial example given by Mark, the PGF lists (a selection of) > probes as "main", while the tra ...
written 4.3 years ago by Mark Cowley910
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Comment: C: pd.hugene.2.0.st missing normgene->exon mappings
... Hi, is it feasible to add a 'type' column to the core_mps table, using info from the transcript csv file? since 'core' implies transcript- level analysis. cheers, Mark On 11/07/2013, at 4:29 AM, cstrato wrote: > Dear Mark, > > Yes, EIF3D and pos_controls mentioned have different transc ...
written 4.4 years ago by Mark Cowley910
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Comment: C: pd.hugene.2.0.st missing normgene->exon mappings
... Hi, I see the point you're making Christian. I'm offline now, so cant check this, but i assume that EIF3D and the pos_control meta-probeset in question have different transcript cluster id's. it doesn't make sense for the pos_control transcript cluster Id to be tagged as 'main'. My grep -f was still ...
written 4.4 years ago by Mark Cowley910
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pd.hugene.2.0.st missing normgene->exon mappings
... Dear Benilton, James & Bioconductors, Thanks for providing the platform design packages for hugene/mogene/ragene 1.0/1.1/2.0/2.1 arrays. I use SQL to query these packages & ultimately retain only 'main' probes in my analysis. This works well for 1.0 and 1.1 packages, but nor for 2.0 and 2.1 ...
cancer probe written 4.4 years ago by Mark Cowley910 • updated 4.4 years ago by James W. MacDonald45k
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Answer: A: Simple question about Vector
... Hi Thiago, have a look at ?ifelse or ?abs cheers, Mark On 26/02/2013, at 10:46 PM, "Thiago [guest]" wrote: > > Hello > > I'm new at bioconductor and I have a very simple and stupid question, but I couldn undertand how to do that. > > I have a vector with a column with negative ...
written 4.7 years ago by Mark Cowley910
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Answer: A: filtering Gene 1.0 ST chips
... Hi Dennis, Here's some code for doing control probe filtering from one of my pipelines cheers, Mark ######################################################### #' Determine the type of each probeset, using data from a Probe Design Info package (eg pd.hugene.1.0.st.v1). #' #' Each probeset is one of ...
written 4.8 years ago by Mark Cowley910
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Comment: C: gdata affects LumiBatch::combine method
... Hi again, Your workaround definitely works in an interactive session, but I was expecting to fix the problem by fixing it within lumi::combine? I rebuilt & installed lumi after removing the recursion within lumi's combine, however even when explicitly calling lumi::combine I still got the error ...
written 5.1 years ago by Mark Cowley910

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