hopach generates a wrong output
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@alogmail2aolcom-4540
Last seen 6.5 years ago

Dear Bioconductor Community,

The last version of the package (HOPACH) generates a wrong output, e.g. using the R code from http://127.0.0.1:14749/library/hopach/html/makeoutput.html

I have received output (please below) from which it is clear that some items clustered to Cluster0 have a much higher cluster membership probability to be in Cluster1 or in Cluster2. From my previous experience, it never happened before in hopach outputs.

Any ideas?

Thanks

Alex 




sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                         
[5] LC_TIME=English_United States.1252   

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] hopach_2.26.0       Biobase_2.26.0      BiocGenerics_0.12.1 cluster_1.15.3    

loaded via a namespace (and not attached):
[1] tools_3.1.2


 

 
Index UID Name Cluster.Number Cluster.Label Cluster.Level.Order Final.Label Final.Level.Order Cluster0.Membership Cluster1.Membership Cluster2.Membership Cluster3.Membership
82 Er.10.100 Er.10.100 0 111 78 1.11E+14 1 0 0 1 0
73 Tm.15.100 Tm.15.100 0 111 73 1.11E+14 2 0 0 1 0
62 Yb.15.100 Yb.15.100 0 111 76 1.11E+14 3 0 0.901 0.099 0
46 Pr.15.50 Pr.15.50 0 111 77 1.11E+14 4 0.001 0.921 0.065 0.013
55 Yb.15.50 Yb.15.50 0 111 75 1.12E+14 5 0 0.766 0.234 0
83 Er.15.100 Er.15.100 0 111 74 1.12E+14 6 0 0.963 0.037 0
34 La.15.50 La.15.50 0 111 72 1.12E+14 7 0 0.144


 

hopach • 685 views
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Can you provide a more reproducible example, perhaps with some simulated data or a subset of your actual data? The following seems to produce consistent results

> example(makeoutput)
​...
> res = read.delim("HOPACH.out", sep="\t")
> apply(res[,grep("Membership", names(res))], 1, which.max) - 1
 [1] 1 0 2 0 0 3 3 0 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
> res$Cluster.Number
 [1] 1 0 2 0 0 3 3 0 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

 

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@alogmail2aolcom-4540
Last seen 6.5 years ago

Yes, I can provide my actual data as input for hopach. Its size is 1MB only. What is best way to send it?

I applied your code to my data and it doesn't produce a consistent result:

res1 = read.delim("conditions.dm.cos.hopach.out", sep="\t")
> dim(res1)
[1] 85 13

> apply(res1[,grep("Membership", names(res1))], 1, which.max) - 1
 [1] 4 4 3 3 0 0 4 4 4 3 3 0 3 4 2 3 1 3 3 3 3 3 3 3 3 3 3 4 4 4 4 3 0 4 3 3 4 0 4 3 4 4 4 4 4 4 4 0 3 3 3 4 0 0 3 2 0 4 4 2 2 3 4 4 3 4 4 4 4 4 3 3 3 3 4 4 0 4 3 3 3 3 3 3 3
> res1$Cluster.Number
 [1] 1 4 4 4 4 1 4 4 4 4 4 4 4 4 4 4 1 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 0 4 4 4 4 0 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 0 4 4 2 2 4 4 4 4 4 4 4 4 4 4 3 3 4 4 4 0 4 4 4 3 4 4 4 4

 

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Post your data to dropbox or similar site (make sure the URL is publicly accessible) and then post the URL here.

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