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Search: Posts Made By: shriram
Forum: Bioinformatics 03-21-2014, 10:38 AM
Replies: 92
Views: 38,219
Posted By shriram
That's great, it makes full sense now, thank you...

That's great, it makes full sense now, thank you very much for your help.
Shriram
Forum: Bioinformatics 03-21-2014, 03:37 AM
Replies: 92
Views: 38,219
Posted By shriram
pv.out.list <- sapply(enriched_pathways,...

pv.out.list <- sapply(enriched_pathways, function(pid) pathview(gene.data = gene_fc, pathway.id = pid, species = "sce", gene.idtype="KEGG", same.layer = F, kegg.native = T, node.sum="median"))
...
Forum: Bioinformatics 03-20-2014, 02:11 AM
Replies: 92
Views: 38,219
Posted By shriram
Thanks for the quick reply. In above example...

Thanks for the quick reply.
In above example GeneA is the only gene [shown green in original kegg] on that node for that species as other genes on the node are not present in the given species....
Forum: Bioinformatics 03-19-2014, 08:00 AM
Replies: 92
Views: 38,219
Posted By shriram
Fold change ploting

Thank you for your reply, now I understand why there are differences at node level data and actual fold changes.
However when I want to compare the fold change that I see in the input data and on...
Forum: Bioinformatics 03-18-2014, 11:09 AM
Replies: 92
Views: 38,219
Posted By shriram
Angry Hi, I was looking at the expression data from...

Hi,
I was looking at the expression data from pathview object and original data supplied to pathview, I found discrepancies in the two values:

Original count data (human data from reference...
Forum: Bioinformatics 03-12-2014, 07:10 AM
Replies: 92
Views: 38,219
Posted By shriram
you have to use cuff.fc instead of exp.fc I...

you have to use cuff.fc instead of exp.fc I guess.
This is R issue as you didn't had this object
Forum: Bioinformatics 02-21-2014, 09:17 AM
Replies: 92
Views: 38,219
Posted By shriram
############ Issue resolved by taking...

############
Issue resolved
by taking substring of actual pathway name in kegg and specifying gene.idtype="KEGG"
path.ids <- substr(path.ids, 1, 8)
############
Forum: Bioinformatics 02-21-2014, 08:04 AM
Replies: 92
Views: 38,219
Posted By shriram
Hi I am using pathview for yeast however I get...

Hi
I am using pathview for yeast however I get following error while retrieving pathway information for 19 different pathways.
[1] "Downloading xml files for sce04113 Meiosis - yeast, 1/19...
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