Unable to make heatmap in CummeRbund

[dipsauce]

Hi all,

I tried to make a heatmap through CummeRbund, but was unable to complete it.

This is what I inserted in R (with output):

> library(cummeRbund)
> cuff_data<-readCufflinks('diff_out')
> mySigGeneIds<-getSig(cuff_data,alpha=0.05,level='genes')
> mySigGenes<-getGenes(cuff_data,mySigGeneIds)
Getting gene information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: no such table: geneReplicateData)

Somehow the geneReplicateData seems to be missing, whereas I originally did have 4 biological replicates per condition.
Is there perhaps a way to bypass the replicate data and still end up with a vector MySigGenes which I can then use for the csHeatmap function?

Thanks in advance for any help!

[TiborNagy]

Try to load cuff_data with rebuild options:
cuff_data <- readCufflinks('diff_out', rebuild=T)

[dipsauce]

Hi TiborNagy,

Thanks for your prompt reply. Your code suggestion worked; I did not get any errors in return.

However, now I am not able to see the final HeatMap, although the data seems intact. Does this perhaps occur because I have approx 3000 significant genes?

> head(fpkm(mySigGenes))
gene_id sample_name fpkm conf_hi conf_lo quant_status stdev
1 XLOC_000010 HZ 0.422422 0.746135 0.0987094 OK 0.1618565
2 XLOC_000010 KO 0.857637 1.115260 0.6000190 OK 0.1288115
3 XLOC_000010 WT 0.213691 0.348188 0.0791939 OK 0.0672485
4 XLOC_000013 HZ 17.163400 20.058400 14.2685000 OK 1.4475000
5 XLOC_000013 KO 8.233930 9.753350 6.7145000 OK 0.7597100
6 XLOC_000013 WT 18.175300 21.145300 15.2052000 OK 1.4850000

> h<-csHeatmap(mySigGenes,cluster='both')
> h

( I then see the picture below... just a white square with grey text)



Thanks once again!

[TiborNagy]

How do you save this image? I guess the parameters of that command caused this.

[dipsauce]

It is actually the image file I see directly in Rstudio after running the script to produce a heatmap..