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Old 11-25-2013, 09:30 AM   #1
wmseq
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Default Why could I not find "kegg.gsets" function in gage package?

Hi bigmw,
I could not find the function of "kegg.gsets" in gage package. Do you have any idea about it?
Was it because I used version 2. 12.0 instead of 2.11.3?
> library(gage)
> ?kegg.gsets
No documentation for ‘kegg.gsets’ in specified packages and libraries:
you could try ‘??kegg.gsets’

Thanks a lot!!

Richard

Last edited by wmseq; 11-25-2013 at 12:53 PM.
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Old 11-25-2013, 06:49 PM   #2
bigmw
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kegg.gsets is a new function introduced into gage since Bioconductor 2.13 (gage version >= 2.12.0).
Make sure you install the current release version here:
http://bioconductor.org/packages/rel...html/gage.html
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Old 11-26-2013, 01:28 AM   #3
wmseq
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Thanks, bigmw!
I am sure I installed it from Bioconducto 2.13.
The commands I used are as follows:
source("http://bioconductor.org/biocLite.R")
biocLite("gage")
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Old 11-26-2013, 06:52 AM   #4
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The the package version biocLite() installs depends on your R/Bioconductor version. To install the current release of bioc packages like gage, you have to make sure your R/Bioconductor version is or newer than 3.0/2.13. To check the status/versions of your bioc packages:
If you are sure you have R version 3.0 or later:
library(BiocInstaller)
biocValid()

If you are not sure, do:
sessionInfo()

I would expect you see outdated R/Bioconductor (and package) versions from above output. To install or update your R/Bioconductor, please check:
http://bioconductor.org/install/
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Old 11-26-2013, 01:48 PM   #5
wmseq
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Hi bigmw,
I have solved the problem. It was because some files in a local directory could not be updated automatically, so that they have to be removed by hand, and than update R.

Now, I can find "kegg.gsets" function, but when I ran the following command, I got another error message.

> kg.ame=kegg.gsets("ame")
Error in korg[ridx, coln] : subscript out of bounds

Do you have any idea on its fixing?

Thanks!

Richard
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Old 11-27-2013, 06:41 AM   #6
bigmw
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The code I give you has been tested across multiple platforms. Below is what I got on my computers. No sure what happened on your side.
You seem to have many odd problems with your computer based on your previous questions/notes. I would suggest you either find another computer or clean up your system (if you can) and resintall the updated R/Bioconductor, gage, pathview and other package from scratch. This will make your work much easier.

> kg.ame=kegg.gsets("ame")
> lapply(kg.ame, head, 3)
$kg.sets
$kg.sets$`ame00010 Glycolysis / Gluconeogenesis`
[1] "408559" "408654" "409624" "409773" "410122" "411140" "411188" "411576" "411897" "412362" "412522" "412843" "413924"
[14] "550687" "550785" "551005" "551039" "551103" "551154" "551631" "552007" "552086" "552678" "552736" "724724" "725455"
[27] "726117" "726225" "727153" "727456"

$kg.sets$`ame00020 Citrate cycle (TCA cycle)`


$sigmet.idx
[1] 76 82 83

$sig.idx
[1] 76 82 83

$met.idx
[1] 1 2 3

$dise.idx
integer(0)
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Old 11-27-2013, 08:43 AM   #7
wmseq
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Thanks a lot, bigmw!
I will consult a computer guy to do it.
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Old 11-27-2013, 03:28 PM   #8
bigmw
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One thing you may also consider is to double check that gage has readlly been updated and successfully reloaded. You may want to restart an R session, and do:
library(gage)
kg.ame=kegg.gsets("ame")

If the same problem still persist, do:
sessionInfo()

and post the output here.
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