Question

hopach generates a wrong output

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Alogmail2@aol.com ▴ 90

@alogmail2aolcom-4540

Last seen 10.0 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 • 1.3k views

ADD COMMENT • link 10.0 years ago • updated 9.9 years ago Alogmail2@aol.com ▴ 90

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Entering edit mode

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

ADD REPLY • link 9.9 years ago Martin Morgan 25k

score 0 · Answer 1 · 2015-01-03

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