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Old 04-23-2012, 08:39 AM   #24
Starr_Hazard
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Location: South Carolina

Join Date: Nov 2010
Posts: 19
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So now I can get gene_short_names from significant TSS ids-- I just cannot plot them

The plot commands I am using are straight out of the cummeRbund manual except that I put them into a for-next loop. Please note that this works fine on getSig output set derived from significant genes set but hangs on isoform and splicing sets.

I examine the ith entry in the set then getGene on that id and make several plots.

I then have a PDF with content or not. The PDF has no messages.

I pipe the output to a text file but that just tells me how far I have gotten.Here are the last lines of output:

> for(i in 1:x) {
+ print(mySigSplicing[i])
+ print(mySplicingGeneShortName[i])
+ print(mySplicingIDs[i])
+ myGeneID<-mySplicingGeneShortName[i]
+ #myGeneID<-mySplicingIDs[i]
+ print(myGeneID)
+ myGene<-getGene(cuff,myGeneID)
+ print(myGene)
+ head(fpkm(myGene))
+ head(fpkm(splicing(myGene)))
+ gl<-expressionPlot(myGene)
+ print(gl)
+ gb<-expressionBarplot(myGene)
+ print(gb)
+ igb<-expressionBarplot(splicing(myGene))
+ print(igb)
+
+ }
[1] "TSS10291"
[1] "Tmem6"
NULL
[1] "Tmem6"
CuffGene instance for gene Tmem6
Short name: Tmem6
Slots:
annotation
fpkm
diff
isoforms CuffFeature instance of size 2
TSS CuffFeature instance of size 1
CDS CuffFeature instance of size 0



There is a screen echo that says:

Error in 'colnames<-'*tmp*,value = "tracking_id"0 :
'names/ attribute[1] must be the same length as the vector [0]
Calls: expressionBarplot-> expressionBarplot->.local ->colnames<-
Execution halted
Warning message:
RS-DBI driver warning (closing pending result sets before closing this connection)

Here is the plotting code again:

x<-length(Sham_vs_Expt.sigIsoforms)
x
print(x)


for(i in 1:x) {
print(Sham_vs_Expt.sigIsoforms[i])
myGeneID<-Sham_vs_Expt.sigIsoforms[i]
myGeneID
myGene<-getGene(cuff,myGeneID)
print(myGene)
head(fpkm(myGene))
head(fpkm(isoforms(myGene)))
gl<-expressionPlot(myGene)
print(gl)
gb<-expressionBarplot(myGene)
print(gb)
igb<-expressionBarplot(isoforms(myGene))
print(igb)

}
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