[BioC] plot QuSAGE problem
Natalia [guest]
guest at bioconductor.org
Mon Nov 18 10:48:11 CET 2013
Dear all,
I would like to quantify gene set differential expression using QuSAGE. When I run qusage a warning is printed because some pathways donât contain any values matching the rownames of eset and the function returns NAs for the values of these pathways. It seems normal according to the manual; however, when I try to plot the results I get this error:
Error en bar.col[p.vals == 0] = c("#00FF00", "#FF0000")[(means > 0) + :
NAs no son permitidos en asignaciones subscritas
As I didnât find any forum discussion related to qusage, to solve this problem I tried to remove columns and/or rows with NAs using different commands from this forum http://stackoverflow.com/questions/4862178/remove-rows-with-nas-in-data-frame that didnât work. Iâve also tried to export the result file to manually remove the NAs values, but I get another error:
Error en data.frame(NUCLEOPLASM = c(40L, 100L, 228L, 255L, 265L, 433L, :
arguments imply differing number of rows: 8, 1, 43, 0, 2, 5, 35, 3, 7, 9, 15, 57, 72, 76, 6, 4, 89, 12, 104, 20, 10, 13, 50, 11, 34, 45, 22, 14, 36, 41, 18, 28, 38, 75, 16, 55, 51, 21, 29, 19, 31, 26, 47, 46, 30, 23, 33, 37, 17, 24
So, I donât know what else I can do. Could you please help me?
Thank you in advance!
Cheers
Natalia
here is my code:
> library("qusage")
Loading required package: limma
> eset <- read.table("CarcinomaLog2b.txt")
> dim(eset)
[1] 670 4
> eset[1:4,1:4]
B1238noCI B898noCI N457CI CIO4CI
ago61 7.246293 7.383201 5.556158 5.646811
ABAT 7.386900 7.473050 5.935872 6.037316
ABCA8 6.423412 6.838683 4.357163 4.706340
ACAP2 7.359547 7.006194 5.658119 5.422421
> labels = c(rep("noCI",2),rep("CI",2))
> labels
[1] "noCI" "noCI" "CI" "CI"
> contrast = "CI-noCI"
> MSIG.geneSets = read.gmt("c5.all.v4.0.symbols.gmt")
> summary(MSIG.geneSets[1:5])
Length Class Mode
NUCLEOPLASM 279 -none- character
EXTRINSIC_TO_PLASMA_MEMBRANE 13 -none- character
ORGANELLE_PART 1197 -none- character
CELL_PROJECTION_PART 19 -none- character
CYTOPLASMIC_VESICLE_MEMBRANE 28 -none- character
> MSIG.geneSets[2]
$EXTRINSIC_TO_PLASMA_MEMBRANE
[1] "GNA14" "APC2" "GNAI1" "SCUBE1" "RGS19" "EEA1" "ARRB1" "TDGF1" "SYTL4" "TGM3" "SYTL2" "GNAS" "SYTL1"
> qs.results.msig = qusage(eset, labels, contrast, MSIG.geneSets)
Calculating gene-by-gene comparisons...Done.
Aggregating gene data for gene sets........................................................................Done.
Calculating variance inflation factors...Done.
There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: In calcIndividualExpressions(eset.2, eset.1, paired = paired, ... :
Some degrees of freedom are below minimum. They have been set to 3.
2: In aggregateGeneSet(results, geneSets, silent = F) :
Gene set: (index 4) has 0 overlap with eset.
3: In aggregateGeneSet(results, geneSets, silent = F) :
Gene set: (index 8) has 0 overlap with eset.
â¦
> p.vals = pdf.pVal(qs.results.msig)
> head(p.vals)
[1] 0.004420964 0.002192533 0.944526837 NA 0.015565253 0.665047012
> q.vals = p.adjust(p.vals, method="fdr")
> head(q.vals)
[1] 0.02186234 0.01575066 0.95799937 NA 0.03560862 0.74452140
> plot(qs.results.msig)
Error en bar.col[p.vals == 0] = c("#00FF00", "#FF0000")[(means > 0) + :
NAs no son permitidos en asignaciones subscritas
> write.table(qs.results.msig, "C:/CarcinomaQusage/qs.results.msig.txt", sep="\t")
Error en data.frame(NUCLEOPLASM = c(40L, 100L, 228L, 255L, 265L, 433L, :
arguments imply differing number of rows: 8, 1, 43, 0, 2, 5, 35, 3, 7, 9, 15, 57, 72, 76, 6, 4, 89, 12, 104, 20, 10, 13, 50, 11, 34, 45, 22, 14, 36, 41, 18, 28, 38, 75, 16, 55, 51, 21, 29, 19, 31, 26, 47, 46, 30, 23, 33, 37, 17, 24
> traceback()
Itâs too long, I only get the final part of it:
â¦
5.2071044013943e-15, 5.19547834250736e-15, 5.18371266247415e-15,
5.1716289962509e-15, 5.16099603768818e-15, 5.15051690240292e-15,
5.14112007625988e-15, 5.13108039263482e-15, 5.12053454327034e-15,
5.10908904454783e-15, 5.09777420691446e-15, 5.08657452313037e-15,
5.07631739482464e-15, 5.06622484767238e-15, 5.0557022518093e-15,
5.04523476479514e-15, 5.0346664383151e-15, 5.02514098459579e-15,
â¦
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
...
vif = c(0.233781854096956, NA,
0.267630050168576, NA, NA, 0.20656384515213, NA, NA, NA,
NA, NA, NA, 0.984323955738163, 1.85096210586702, 1.68418716723949,
NA, NA, NA, NA, NA, NA, 1.29506034501887, 1.6117330327914,
NA, 0.0769539109044178, 2.3903824686852, NA, NA, NA, 1.56236758547383,
0.320770501799159, 0.912003653287104, 0.672521204303017,
NA, 1.03652420528229, NA, 1.02504640850195, 1.09865040867118,
NA, NA, 1.83839137148713, 2.18615700744765, NA, NA, NA, 1.75828917222515,
...
6: eval(expr, envir, enclos)
5: eval(as.call(c(expression(data.frame), x, check.names = !optional,
stringsAsFactors = stringsAsFactors)))
4: as.data.frame.list(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
3: as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
2: data.frame(x)
1: write.table(qs.results.msig, "C:/CarcinomaQusage/qs.results.msig.txt",
sep = "\t")
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C LC_TIME=Spanish_Spain.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] qusage_1.2.0 limma_3.18.2
loaded via a namespace (and not attached):
[1] Biobase_2.22.0 BiocGenerics_0.8.0 parallel_3.0.2
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