User: Rich Savage

gravatar for Rich Savage
Rich Savage60
Reputation:
60
Status:
Trusted
Location:
University of Warwick, UK
Website:
http://www2.warwick.ac...
Twitter:
@WarwickDataSci
Last seen:
4 years, 1 month ago
Joined:
11 years ago
Email:
r*********@warwick.ac.uk

Posts by Rich Savage

<prev • 8 results • page 1 of 1 • next >
1
vote
1
answer
751
views
1
answers
Answer: A: BHC crashes on a 100 samples and 4 variables
... Hi Jairo, I believe the reason for the crash is that you're giving BHC real-valued data for the default data model (which is multinomial, so requires discrete values).  The documentation for the 'bhc' function gives an example of how to discretise your data.  Adapting that, you could try the follow ...
written 4.3 years ago by Rich Savage60
0
votes
1
answer
655
views
1
answers
Answer: A: Heatmaps in BHC package
... Try something like the following: hc3 <- bhc(discreteData, rowLabels, verbose = T) hc2 <- bhc(t(discreteData), colLabels, verbose = T) heatmap.2(discreteData, trace="none", hclustfun = function(x) hclust(x,"ave"),col=redgreen(100),breaks=colors,Rowv = hc2,Colv=hc3) ...
written 4.5 years ago by Rich Savage60
0
votes
1
answer
772
views
1
answers
Answer: A: BHC breaks on simple dataset
... Hi folks, I believe problem you are seeing is because the toy data you're inputting has 4 unique values {1,2,3,5}, but isn't using {1,2,3,4}.  I'm afraid that for N classes in the multinomial version of BHC, you need to use the numerical values 1:N I'm not sure when the next update to BHC will hap ...
written 4.5 years ago by Rich Savage60
0
votes
2
answers
487
views
2
answers
Comment: C: BHC appears to be broken
... Dear Joseph, I believe the problem is that you're calling 'bhc' incorrectly. There is a legacy value that needs to be entered as the 3rd input, which you're missing (see below). Apologies for the presence of this - it's no longer required by the algorithm, but is there to prevent people's scripts ...
written 6.5 years ago by Rich Savage60
0
votes
1
answer
709
views
1
answers
Answer: A: Error when trying to build a package that needs to import GO.db, GOstats, ath112
... Hi Martin, That worked perfectly! Thanks :-) I added the following line to my NAMESPACE file: importMethodsFrom(AnnotationDbi, eapply) Plus, I changed my DESCRIPTION file to include this dependency: Depends: methods, BHC, GO.db, GOstats, ath1121501.db, AnnotationDbi ('BHC' is my own package ...
written 11.0 years ago by Rich Savage60
0
votes
0
answers
630
views
0
answers
Error when trying to build a package that needs to import GO.db, GOstats, ath1121501.db packages
... Hi all, I am trying to build a small package that contains some specific functions to perform GO annotation and have encountered an error when running 'R CMD check' on the package I (try to) build. Specifically: [1] "S4" Length Class Mode 25369 GO ...
annotation go ath1121501 bhc written 11.0 years ago by Rich Savage60
0
votes
1
answer
662
views
1
answers
Comment: C: Encountering error when using GOstats package
... Hi Vincent, Thanks for your reply. I uninstalled the non-SQLite package using: > remove.packages('ath1121501') I then re-ran the code I posted. Still got the error :-( (new sessionInfo also posted below) Error in get(mapName, envir = pkgEnv, inherits = FALSE) : variable "ath1121501ENTR ...
written 11.1 years ago by Rich Savage60
0
votes
1
answer
662
views
1
answer
Encountering error when using GOstats package
... Hi all, I'm using the GOstats package to find significant GO terms. This has been working fine but I've just upgraded to the R version 2.7.2 (and the latest versions of the Bioconductor packages) and I now get an error. I've had no luck trying to fix this and so am hoping someone an help me! EX ...
go ath1121501 gostats written 11.1 years ago by Rich Savage60 • updated 11.1 years ago by Vincent J. Carey, Jr.6.3k

Latest awards to Rich Savage

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 393 users visited in the last hour