Hi Wejun,

I am new to BIOC and Pathview/Gage packages. I am analysing microarray data from an experiment on Atlantic salmon and I am attempting to visualize the results in Pathview, if possible.

Following up a previous thread (https://stat.ethz.ch/pipermail/bioconductor/2013-August/054161.html), I have been trying to do a similar thing and I believe I have similar limitation. As for the previous user, I have obtained KEGG Orthology annotation using KAAS. Briefly, the principal steps of my workflow look like the following:

> DIET12_14_KO <- read.csv("DIET12_14_KO.csv",header=T, sep=",") # Upload the KEGG annotation file from KAAS
> DIET12_14_KO[1:3,]
     ProbeName     KO
1 Omy#AB024321 K04079
2 Omy#BG360545 K13506
3 Omy#BX072887 K00412
> MAlist[1:3,1:6] # Visualize my expression list
                  DIET14    DIET14.1   DIET14.2   DIET14.3      DIET02    DIET02.1
Omy#AB024321  0.06296557  0.08865075  0.1186315 -0.1847021 -0.41212414 -0.42385673
Omy#BG360545 -0.50762181 -0.35763304 -0.4939668 -0.6973216 -0.11339368  0.15489712
Omy#BX072887  0.23447458  0.22487856  0.3930821  0.1515031 -0.04694996 -0.04836203
> dim(MAlist)
[1] 7955   16
> D2 <- as.matrix(DIET12_14_KO) # create the two column character matrix for id.map argument
> D2[1:3,]
     ProbeName      KO
[1,] "Omy#AB024321" "K04079"
[2,] "Omy#BG360545" "K13506"
[3,] "Omy#BX072887" "K00412"
> gene.data <- mol.sum(MAlist, id.map = D2)
> gene.data [1:3,1:6]
           DIET14     DIET14     DIET14     DIET14       DIET02     DIET02
K00006  0.7170382  0.5351467  0.1207924  0.1782242  0.228860514 -0.5426538
K00008 -0.8112601 -0.5910453 -0.7691811 -0.1919992 -0.003848065  0.1771637
K00011  1.9645823  1.2305297  2.3335377  1.4813718  0.185036373 -1.2886788
> dim(gene.data)
[1] 2449   16

I am a bit stuck here. I should now have the data in the correct format for the pathview argument "gene.data" with genes as row and samples as column and KO ids as row names. From my understanding, to proceed I will now need a KO gene set data for non-model species? Or could I use one from a close species like zebrafish?

Also, one thing I have not clear is if the gene.data should include the expression values of all sample (i.e. biological replicates) or the average value per treatment.

Your help will be very much appreciated.

Regards,
Christian




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