User: J.delasHeras@ed.ac.uk

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Posts by J.delasHeras@ed.ac.uk

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Comment: C: convert gene name to Affy ID
... Hi Julia, if you check the list of annotation packages already made in the Bioconductor page http://www.bioconductor.org/packages/release/BiocViews.html#___Annotat ionData you may find your array there. I don't know if this will be your array, but just for illustration purposes, I see that the a ...
written 4.9 years ago by J.delasHeras@ed.ac.uk1.9k
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Answer: A: need help regarding microarray data analysis using limma
... Quoting varshika singh on Thu, 13 Dec 2012 11:02:15 +0530: > Dear Sir/Madam > I am using bioconductor package for analysis of Agilent two color data. > After normalisation when i am giving command dat.m<-dat2$M, an error is > shown as: > Error in dat2$M : $ operator is invalid f ...
written 4.9 years ago by J.delasHeras@ed.ac.uk1.9k
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Answer: A: Duplicate probes
... Quoting Ed Siefker on Wed, 21 Mar 2012 11:20:17 -0500: > I am analyzing affymetrix hgu133plus2 arrays with limma. > These arrays sometimes contain multiple probes for a > single gene. I would like to combine the readings so that > I get exactly one estimate of fold change per (entrez) ...
written 5.7 years ago by J.delasHeras@ed.ac.uk1.9k
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Comment: C: GEOquery: how to extract experimental data? (confused)
... Quoting Vincent Carey on Tue, 16 Aug 2011 07:38:19 -0400: > you have noted that getGEO returns a list, and the first element of the list > you got is an ExpressionSet instance. > > you are asking about access to the assayData. This concerns ExpressionSet > mechanics, not GEOquery & ...
written 6.3 years ago by J.delasHeras@ed.ac.uk1.9k
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Comment: C: GEOquery: how to extract experimental data? (confused)
... Quoting Sean Davis on Tue, 16 Aug 2011 07:36:41 -0400: > On Tue, Aug 16, 2011 at 7:20 AM, wrote: >> >> I have been until now downloading GEO data directly to my computer and using >> basic R functions to load tables and process them. >> It works, but I figured I would ...
written 6.3 years ago by J.delasHeras@ed.ac.uk1.9k
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GEOquery: how to extract experimental data? (confused)
... I have been until now downloading GEO data directly to my computer and using basic R functions to load tables and process them. It works, but I figured I would probably save time if I learn to use the GEOquery package, which looks promising. However, I'm failing tremendously at my first attempt. I ...
process geoquery written 6.3 years ago by J.delasHeras@ed.ac.uk1.9k • updated 6.3 years ago by Dai, Hongying,60
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Comment: C: GOstats with Reactome database?
... Quoting Martin Morgan on Mon, 15 Aug 2011 10:11:50 -0700: > On 08/15/2011 05:48 AM, J.delasHeras at ed.ac.uk wrote: >> Dear all, >> >> with the demise of KEGG (well, at least without subscription), I was >> wondering whether there are any plans to get GOstats working wit ...
written 6.3 years ago by J.delasHeras@ed.ac.uk1.9k
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GOstats with Reactome database?
... Dear all, with the demise of KEGG (well, at least without subscription), I was wondering whether there are any plans to get GOstats working with the Reactome database, or whether there is an "easy" way to persuade GOstats to work with it. Any ideas? Jose -- Dr. Jose I. de las Heras ...
gostats written 6.3 years ago by J.delasHeras@ed.ac.uk1.9k • updated 6.3 years ago by Martin Morgan ♦♦ 20k
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Comment: C: biomaRt: using a list as values. confused...
... THat's probably a good idea. Most people would realise the result is not the expected one, but it will be better to find an error and be safe. thank you! Jose Quoting Steffen Durinck on Thu, 9 Jun 2011 09:40:41 -0700: > Hi Jose, > > I'll make biomaRt throw an error when someone tries ...
written 6.4 years ago by J.delasHeras@ed.ac.uk1.9k
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Comment: C: biomaRt: using a list as values. confused...
... Hi Stephen, many thanks for that. I was looking at the previous results that I said were ok and realised the ranges were wrong and that confused me even more! Thanks for teh tip about the chromosomal region, that's just what I needed! Jose Quoting Steffen Durinck on Thu, 9 Jun 2011 09:12:59 - ...
written 6.4 years ago by J.delasHeras@ed.ac.uk1.9k

Latest awards to J.delasHeras@ed.ac.uk

Popular Question 2.3 years ago, created a question with more than 1,000 views. For GEOquery: how to extract experimental data? (confused)
Centurion 4.9 years ago, created 100 posts.

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