User: J.delasHeras@ed.ac.uk

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Posts by J.delasHeras@ed.ac.uk

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Comment: C: removing packages from the workspace - is this ok?
... thank you, I was not aware of ls() being able to return these data. Jose Quoting "Harris A. Jaffee" on Thu, 9 Jun 2011 09:15:22 -0400: > This will get you started, but it's probably not the full answer. > > ? getAnywhere > ? ls > > For example, ls(2), but note that this conta ...
written 8.4 years ago by J.delasHeras@ed.ac.uk1.9k
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Comment: C: Use of individual channel from a 2-color array as a measure of expression level?
... Hi Hari, then I misunderstood what you were trying to do, and Limma will be a great tool indeed, whether as a two-channel or one-channel mode :) Jose Quoting Hari Easwaran on Thu, 9 Jun 2011 11:33:55 -0400: > Hi Jim and Jose, > Thanks a lot. I will check the limma user guide. > > ...
written 8.4 years ago by J.delasHeras@ed.ac.uk1.9k
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biomaRt: using a list as values. confused...
... I'm trying to obtain information about genes within a number of regions defined by a chromosome name, start and end coordinates. I understand that the way to specify multiple filters to be used together (a set of chr+start+end) is to use a list for 'values'. This seems to work ok when I have more ...
written 8.4 years ago by J.delasHeras@ed.ac.uk1.9k • updated 8.4 years ago by Steffen Durinck540
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Comment: C: removing packages from the workspace - is this ok?
... Hi Herve, this indeed was the issue I had, which works perfectly well by following Steve's suggestion: simply explicitly renaming objects to ensure one deals with the correct one. The idea of explicitly indicating the package using the double semicolon had escaped me too, so thank you for bringing ...
written 8.4 years ago by J.delasHeras@ed.ac.uk1.9k
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Answer: A: Use of individual channel from a 2-color array as a measure of expression level?
... Quoting Hari Easwaran on Wed, 8 Jun 2011 12:42:12 -0400: > Dear BioC gurus, > > Two-color arrays are generally used to compare expression of a test sample > (like drug treated) relative to control. Usually Cy5 channel is used for the > test and Cy3 is used for the control. The outpu ...
written 8.4 years ago by J.delasHeras@ed.ac.uk1.9k
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removing packages from the workspace - is this ok?
... This is more of a general R question, but it concerns in this case genomic annotation packages (BSgenome) and I would like to be sure I'm using this correctly and not mudling things up inadvertently. As part of certain checks I'm running, using various IDs and coordinates from different genomic bu ...
annotation process written 8.4 years ago by J.delasHeras@ed.ac.uk1.9k • updated 8.4 years ago by Steve Lianoglou12k
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Comment: C: Any changes in Biomart regarding GO terms? Script crashing today
... Hi Rhoda, thank you for the explanation. I notice the description of the attributes contain a "(bp)" in them: GO Term Accession (bp) GO Term Name (bp) GO Term Definition (bp) GO Term Evidence Code (bp) Initially I thought it mean they referred to Biological Process and that CC and MF were missi ...
written 8.5 years ago by J.delasHeras@ed.ac.uk1.9k
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Comment: C: Any changes in Biomart regarding GO terms? Script crashing today
... Hi Steffen, thank you for your fast reply. Indeed, after I posted my message I looked into the attributes and found that there are "generic" GO attributes (although their description included a "(bp)" which at first I took to mean they referred to "biological process" and I was looking for the (mf ...
written 8.5 years ago by J.delasHeras@ed.ac.uk1.9k
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Any changes in Biomart regarding GO terms? Script crashing today
... I am unable to run a script I have been using quite happily in the past, so I suspect a change in the "outside world", but I can't find any news about it. It appears that the usual attributes for GO terms and IDs (CC, BP and MF) are not available. (?) If you try this quick example: library(bioma ...
go biomart written 8.5 years ago by J.delasHeras@ed.ac.uk1.9k • updated 8.5 years ago by Steffen Durinck540
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Comment: C: problems connecting to Biomart today?
... Quoting Rhoda Kinsella : > Hi Jose > I should also have mentioned in my previous email that if you are > having difficulties doing other queries, this may be a server issue > at www.biomart.org and you should try running your query against > www.ensembl.org marts by setting host=www. ...
written 8.7 years ago by J.delasHeras@ed.ac.uk1.9k

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

Great Question 4.2 years ago, created a question with more than 5,000 views. For GEOquery: how to extract experimental data? (confused)
Popular Question 4.2 years ago, created a question with more than 1,000 views. For biomaRt: using a list as values. confused...
Popular Question 4.2 years ago, created a question with more than 1,000 views. For GEOquery: how to extract experimental data? (confused)
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Any changes in Biomart regarding GO terms? Script crashing today
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Limma: correct calculation of B statistics (log odds)
Popular Question 4.2 years ago, created a question with more than 1,000 views. For GEOquery: how to extract experimental data? (confused)
Centurion 6.9 years ago, created 100 posts.

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