The reason that you got errors using your data was no significant term was
found. I will add a error message for this error. One fast solution for your
problem is to increase "fdrth" to 0.1 and you may found significant terms
under this threshold.

I also used interestGenes[1:2225] and interestGenes[1:2228] to run
GOFunction and I did not get any error and the bmp file also contained DAG
plot. So, I am not sure why you got the error.

Thanks,
Jing Wang

> 
> When I use GOFunction package to analyse my data with 94 interestGenes and 265
> refGenes, it report an error:`[<-.data.frame`(`*tmp*`, sigTerm[, 1] %in%
> noRelationTerm, 7, :
> replacement has 1 rows, data has 0
> and a warining about in max(i)...
> I look into the function, find the sigTerm has nothing:
>> > sigTerm
> [1] goid name refnum interestnum pvalue adjustp
> <0 rows> (or 0-length row.names)
> I use the exampledata to do it again, it runs OK. But I select part of genes
> in the interestGenes such as x <- interestGenes[1:2225] then use x as
> interestGenes to run
> sigTerm <- GOFunction(x, refGenes, ontology="BP", filename="SigTerm"), it runs
> OK. The output file sigTerm.bmp has 3908KB while nothing in it.
> I run x <- interestGenes[1:2228] and sigTerm <- GOFunction(x, refGenes,
> ontology="BP", filename="SigTerm") it also report errors like the above for
> another reason. I am confused why it is only perfect when use the exampledata
> while others are not. Can you figure out the error and help me to solve the
> problem?
> system:win7
> GOFunction:v2.9
> 
> -- output of sessionInfo():
> 
> Finding statistically significant terms...
> Treating for local redundant terms...
> 閿欒浜巂[<-.data.frame`(`*tmp*`, sigTerm[, 1] %in% noRelationTerm, 7, :
> replacement has 1 rows, data has 0
> 姝ゅ: 璀﹀憡淇℃伅锛
> In max(i) : max閲屾墍鏈夌殑鍙傛暟閮戒笉瀛樺湪锛涘洖瑕-Inf
> 
> 
> Finding statistically significant terms...
> Treating for local redundant terms...
> 閿欒浜巌f (pc > pcth) sigTerm[sigTerm[, 1] %in% activeChild, 8] <-
> sigTerm[sigTerm[, :
> 闇瑕乀RUE/FALSE鍊肩殑鍦版柟涓嶅彲浠ョ敤缂哄皯鍊
> 姝ゅ: 璀﹀憡淇℃伅锛
> In phyper(length(allcsiggenes) - 1, length(sgenes), length(genes) - :
> 浜х敓浜哊aNs
> 
> 
> --
> Sent via the guest posting facility at bioconductor.org.



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