Forum: Bioinformatics
11-08-2014, 02:18 PM
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Replies: 0
Views: 1,341
No GO terms in goseq output
Hi,
I am doing goseq on RNA-seq data of S. pombe. Below I am showing the last few lines of calculating the enriched GOs for my up-regulated genes. In the GO.hyper_up I don't get two last columns...
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Forum: RNA Sequencing
10-28-2014, 02:08 AM
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Replies: 4
Views: 2,219
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Forum: Bioinformatics
10-28-2014, 02:00 AM
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Replies: 3
Views: 1,351
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Forum: Bioinformatics
10-27-2014, 02:03 PM
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Replies: 4
Views: 1,649
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Forum: Bioinformatics
10-23-2014, 06:36 AM
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Replies: 8
Views: 2,102
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Forum: Bioinformatics
10-23-2014, 05:45 AM
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Replies: 8
Views: 2,102
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Forum: Bioinformatics
10-23-2014, 04:46 AM
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Replies: 8
Views: 2,102
Yes and it gives error:
>...
Yes and it gives error:
> library(AnnotationForge)
> makeOrgPackageFromNCBI(tax_id="4896")
Error in .isSingleString(version) :
argument "version" is missing, with no default
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Forum: Bioinformatics
10-23-2014, 12:17 AM
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Replies: 8
Views: 2,102
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Forum: Bioinformatics
10-22-2014, 12:01 PM
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Replies: 8
Views: 2,102
makeOrgPackageFromNCBI for S. pombe
Hi,
Does anybody know where to look up for these parameters required for the following function? No matter how much I searched on NCBI I couldn't find it! My organism is schizosaccharomyces pombe.
...
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Forum: Bioinformatics
09-18-2014, 08:23 AM
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Replies: 4
Views: 1,291
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Forum: Bioinformatics
09-17-2014, 01:38 AM
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Replies: 4
Views: 1,291
No this one is different! The answer to the...
No this one is different! The answer to the transcriptDB post helped a lot. This one is GO annotations! Aren't them different?
I have another post with more detailed information here...
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Forum: Bioinformatics
09-16-2014, 03:57 AM
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Replies: 4
Views: 1,291
GO dataset for s. pombe
Hi,
I am willing to do GO analysis on my RNA-seq data from S. pombe organism. As far as I understood "gageData" package doesn't hold the data set for S. pombe. So I could find the data set on...
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Forum: Bioinformatics
07-07-2014, 01:27 AM
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Replies: 4
Views: 1,649
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Forum: Bioinformatics
06-23-2014, 01:41 AM
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Replies: 1
Views: 1,716
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Forum: Bioinformatics
06-22-2014, 05:55 AM
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Replies: 15
Views: 12,454
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Forum: Bioinformatics
06-21-2014, 05:33 AM
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Replies: 15
Views: 12,454
Thanks a million bigmw, it made it work. I had...
Thanks a million bigmw, it made it work. I had read the pathview tutorial before but I couldn't figure out that part very well! You made it clear to me. And yes about the path.ids2 I could figure...
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Forum: Bioinformatics
06-20-2014, 01:59 AM
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Replies: 15
Views: 12,454
Thanks a million bigmw, it worked! At least it...
Thanks a million bigmw, it worked! At least it downloaded the pathways I mean, but still there are some issues. Regarding R I am learning it, but still it's a very big subject that the pace of...
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Forum: Bioinformatics
06-19-2014, 03:14 PM
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Replies: 15
Views: 12,454
> head(fc.kegg.p$greater)
...
> head(fc.kegg.p$greater)
p.geomean stat.mean p.val
spo03013 RNA transport 0.002445005 2.852610 0.002445005
spo00330 Arginine...
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Forum: Bioinformatics
06-19-2014, 12:48 PM
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Replies: 15
Views: 12,454
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Forum: Bioinformatics
06-19-2014, 02:18 AM
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Replies: 15
Views: 12,454
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Forum: Bioinformatics
06-18-2014, 02:23 AM
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Replies: 15
Views: 12,454
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Forum: Bioinformatics
06-18-2014, 01:21 AM
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Replies: 15
Views: 12,454
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Forum: Bioinformatics
06-17-2014, 03:03 PM
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Replies: 2
Views: 1,711
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Forum: Bioinformatics
06-16-2014, 04:46 AM
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Replies: 2
Views: 1,711
Zero output for sel.rn=rowSums(cnts) != 0
I get a problem when I want to try step 2 from "RNA-seq data pathway and gene-set analysis workflow" by Weijun Luo. I get zero rows with value !=0.
> p.cnts=assay(gnCnt)
> cnts=p.cnts
>...
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Forum: Bioinformatics
06-11-2014, 10:46 AM
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Replies: 3
Views: 1,774
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