I have been attempting to obtain a list of differentially expressed genes from a pairwise comparison of microarray data. I am running into an error when calling the get.annotation function from package: "simpleaffy" because the object I call it on has no probe-sets in the calls slot of the PairComp object. This occurs even though the tt slot which includes t-test values between groups does seemingly have probe-sets. If anyone has any insights about this issue, I would really appreciate it!
> summary <- results.summary(pw.filtered, "hgu133plus2.db")
hgu133plus2.db -cdfname1NULL
hgu133plus2 -cdfnameNULL
Error in mget(x, envir = get(paste(cdfname, "SYMBOL", sep = "")), ifnotfound = list(simpleaffy:::.if.probeset.not.found)) :
only NA is currently supported for 'ifnotfound'
>pw.filtered
3.811797e-04 1.307617e-02 2.166568e-04 8.291114e-04
37547_at 37549_g_at 37892_at 37950_at
3.818242e-03 7.050013e-03 7.331992e-05 4.211978e-03
38037_at 38149_at 39248_at 39249_at
5.177551e-05 3.071316e-02 1.483113e-03 1.732506e-02
39402_at 41512_at 41660_at 45297_at
5.762073e-03 1.370193e-02 5.776765e-03 7.799225e-04
45714_at 50221_at 51226_at 53991_at
4.207862e-04 2.384170e-03 8.849272e-03 6.814868e-05
57715_at 64408_s_at 65472_at 65517_at
3.240915e-03 2.841543e-02 1.042202e-02 1.073591e-03
AFFX-M27830_3_at
2.282442e-02
Slot "calls":
<0 x 0 matrix>
Slot "group":
[1] "treatment"
Slot "members":
[1] "n" "a"
Slot "pData":
sample treatment
GSM190178.CEL 1 n
GSM190179.CEL 2 n
GSM190180.CEL 3 n
GSM190185.CEL 4 a
GSM190186.CEL 5 a
Slot "calculated.from":
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 5 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM190178.CEL GSM190179.CEL ... GSM190186.CEL (5 total)
varLabels: sample treatment
varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: hgu133plus2
Best,
Matthew P. Grieshop
University of Wisconsin
Department of Biochemistry