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Forum: RNA Sequencing 05-21-2014, 01:54 AM
Replies: 2
Views: 1,866
Posted By shriram
did you got any reply on this, I have similar...

did you got any reply on this, I have similar issue with TopHat
Cheers,
Shriram
Forum: Bioinformatics 03-21-2014, 10:38 AM
Replies: 92
Views: 35,831
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: 35,831
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: 35,831
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: 35,831
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: 35,831
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: 35,831
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: 35,831
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: 35,831
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...
Forum: Bioinformatics 12-31-2013, 06:36 AM
Replies: 25
Views: 19,398
Posted By shriram
CNVnator installation

This is what I have in my LD_LIBRARY_PATH
LD_LIBRARY_PATH=/compilers/gcc/4.3.5//lib:/compilers/gcc/4.3.5/lib64:${ROOTSYS}/lib
Forum: General 05-25-2012, 07:52 AM
Replies: 2
Views: 2,572
Posted By shriram
You need to provide the gtf/gff file to tophat...

You need to provide the gtf/gff file to tophat and cufflinks to get the known genes structure + novel genes.
Forum: Bioinformatics 03-23-2012, 05:40 AM
Replies: 25
Views: 19,398
Posted By shriram
Unable to install the CNVnator, I get following...

Unable to install the CNVnator, I get following errors

g++ -pthread -m64 -DCNVNATOR_VERSION=\"v0.2.5\" -I:/nexsan/sbhosle/software/root/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
In...
Forum: Bioinformatics 05-07-2010, 03:04 AM
Replies: 48
Views: 51,115
Posted By shriram
Hello new to the group

Hello new to the group
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