[BioC] problem with CoCiteStats in bioC 1.8

[Kimpel, Mark William]

I am getting an error when using the function "gene.geneslist.sig" from the package CoCiteStats. The code that generates this error, along with sessionInfo, is below.

Suggestions? Thanks,

Mark


> comm.gene.mat.same.annot[98,6]
[1] "29527"
> comm.gene.mat.same.annot[-98,6]
  [1] "25270"  "25364"  "25288"  "117243" "312670" "26956"  "140667" "64312"  "54225"  "287774" "79121"  "293152" "25612"  "81643"  "114766" "24888" 
 [17] "64473"  "24227"  "29687"  "29681"  "29156"  "25298"  "83689"  "25621"  "54237"  "113960" "81925"  "24253"  "24259"  "60384"  "171547" "25420" 
 [33] "89808"  "25086"  "25251"  "25429"  "79128"  "81653"  "83687"  "81654"  "300721" "24329"  "24356"  "84384"  "81659"  "81660"  "116686" "24423" 
 [49] "81675"  "171155" "25632"  "25735"  "83498"  "84013"  "288444" "25587"  "25585"  "25663"  "83523"  "81677"  "292028" "25327"  "59324"  "24903" 
 [65] "25328"  "29236"  "65172"  "171447" "64862"  "58960"  "81649"  "64370"  "29254"  "81686"  "81710"  "116632" "288475" "25499"  "59315"  "93667" 
 [81] "114115" "117287" "25604"  "25737"  "54133"  "65152"  "25344"  "25046"  "60376"  "296588" "286988" "64367"  "24666"  "24672"  "301323" "24686" 
 [97] "29676"  "50646"  "29463"  "245964" "29304"  "65137"  "25271"  "116635" "308993" "25715"  "25550"  "25176"  "25552"  "24791"  "24796"  "64456" 
[113] "25557"  "59267"  "24818"  "29610"  "64524"  "24851"  "81815"  "25274"  "81920"  "25361"  "83785"  "25696"  "301549" "56011"  "25578" 
> gene.geneslist.sig(gene=comm.gene.mat.same.annot[98,6], geneslist=comm.gene.mat.same.annot[-98,6], n.resamp=100)
Error in wh$papers[[g1]] : subscript out of bounds

Enter a frame number, or 0 to exit   

1: gene.geneslist.sig(gene = comm.gene.mat.same.annot[98, 6], geneslist = comm.gene.mat.same.annot[-98, 6], n.resamp = 100)
2: gene.geneslist.statistic(gene, geneslist, numPapers, PaperLen)
3: gene.gene.statistic(gene, i, numPapers, PaperLen)
4: twowayTable(g1, g2, weights = FALSE, numPapers)

Selection: c
Enter an item from the menu, or 0 to exit
Selection: 0
> sessionInfo()
Version 2.3.0 Under development (unstable) (2006-03-24 r37571) 
i386-pc-mingw32 

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

other attached packages:
    CoCiteStats humanLLMappings      reposTools          rgu34a       rgu34acdf            affy          affyio         Biobase         RWinEdt 
        "1.4.0"         "1.8.1"        "1.10.0"        "1.12.0"        "1.12.0"        "1.10.0"         "1.0.0"        "1.10.0"         "1.7-4"

Mark W. Kimpel MD 

 
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