GOFunction error
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Last seen 6.8 years ago
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... ?????????[<-.data.frame(*tmp*, sigTerm[, 1] %in% noRelationTerm, 7, : replacement has 1 rows, data has 0 ??????: ??????????????? In max(i) : max???????????????????????????????????????-Inf Finding statistically significant terms... Treating for local redundant terms... ?????????if (pc > pcth) sigTerm[sigTerm[, 1] %in% activeChild, 8] <- sigTerm[sigTerm[, : ??????TRUE/FALSE????????????????????????????????? ??????: ??????????????? In phyper(length(allcsiggenes) - 1, length(sgenes), length(genes) - : ?????????NaNs -- Sent via the guest posting facility at bioconductor.org.
GOFunction GOFunction • 761 views
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Jing Wang ▴ 10
@jing-wang-5523
Last seen 4.2 years ago
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... > é¿æ¬æµå·[<-.data.frame(*tmp*`, sigTerm[, 1] %in% noRelationTerm, 7, : > replacement has 1 rows, data has 0 > å§ã : çï¹æ¡æ·âä¼ é > In max(i) : maxé²å±¾å¢éå¤æ®éåæé®æç¬çæ¨ºæ¹ªéæ¶æ´ç-Inf > > > Finding statistically significant terms... > Treating for local redundant terms... > é¿æ¬æµå·f (pc > pcth) sigTerm[sigTerm[, 1] %in% activeChild, 8] <- > sigTerm[sigTerm[, : > éçä¹RUE/FALSEéè©æ®é¦çææ¶å¶ å½²æµ ã§æ¤ç¼åç¯é > å§ã : çï¹æ¡æ·âä¼ é > In phyper(length(allcsiggenes) - 1, length(sgenes), length(genes) - : > æµÑ ææµåaNs > > > -- > Sent via the guest posting facility at bioconductor.org. [[alternative HTML version deleted]]