SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 84
Search took 0.03 seconds.
Search: Posts Made By: Parharn
Forum: Bioinformatics 11-08-2014, 02:18 PM
Replies: 0
Views: 1,325
Posted By Parharn
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...
Forum: RNA Sequencing 10-28-2014, 02:08 AM
Replies: 4
Views: 2,176
Posted By Parharn
I do DESeq2, have you tried that? And what is...

I do DESeq2, have you tried that?
And what is your organism?
Forum: Bioinformatics 10-28-2014, 02:00 AM
Replies: 3
Views: 1,337
Posted By Parharn
Hi Roger, Yes I managed to do some GO enrichment...

Hi Roger, Yes I managed to do some GO enrichment analysis and pathway analysis on it! Thanks for asking. Do you suggest anything else?
Forum: Bioinformatics 10-27-2014, 02:03 PM
Replies: 4
Views: 1,617
Posted By Parharn
Yes, later I discovered it but thanks to saying...

Yes, later I discovered it but thanks to saying anyway :)
Forum: Bioinformatics 10-23-2014, 06:36 AM
Replies: 8
Views: 2,071
Posted By Parharn
All right I posted it to their support site now....

All right I posted it to their support site now. However if you are familiar with goseq I would like to ask you to have a look on this thread (https://www.biostars.org/p/116483/)I have another...
Forum: Bioinformatics 10-23-2014, 05:45 AM
Replies: 8
Views: 2,071
Posted By Parharn
Thanks, I thought that is given as example. Now...

Thanks, I thought that is given as example. Now it worked but still I receive an error I don't know how to resolve. Can you help in that?

> makeOrgPackageFromNCBI(version = "0.1", author = "Some...
Forum: Bioinformatics 10-23-2014, 04:46 AM
Replies: 8
Views: 2,071
Posted By Parharn
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
Forum: Bioinformatics 10-23-2014, 12:17 AM
Replies: 8
Views: 2,071
Posted By Parharn
Yes but it requires all the parameters in order...

Yes but it requires all the parameters in order to make package.
Version, author maintainer, etc.
Forum: Bioinformatics 10-22-2014, 12:01 PM
Replies: 8
Views: 2,071
Posted By Parharn
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.
...
Forum: Bioinformatics 09-18-2014, 08:23 AM
Replies: 4
Views: 1,274
Posted By Parharn
Thanks a lot!

Thanks a lot!
Forum: Bioinformatics 09-17-2014, 01:38 AM
Replies: 4
Views: 1,274
Posted By Parharn
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...
Forum: Bioinformatics 09-16-2014, 03:57 AM
Replies: 4
Views: 1,274
Posted By Parharn
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...
Forum: Bioinformatics 07-07-2014, 01:27 AM
Replies: 4
Views: 1,617
Posted By Parharn
Question: How to merge replicates of mapped reads out of Tophat for pathview and gage

Hi, I have three biological replicates for my experiment. I wonder how should I merge the accepted_hits.bam out of Tophat for doing Pathview/gage analysis for "RNA-seq Pathway and Gene-set analysis...
Forum: Bioinformatics 06-23-2014, 01:41 AM
Replies: 1
Views: 1,706
Posted By Parharn
The answer I got here...

The answer I got here (https://www.biostars.org/p/103251/).
Forum: Bioinformatics 06-22-2014, 05:55 AM
Replies: 15
Views: 12,397
Posted By Parharn
I have one more question! In part 6.5 of...

I have one more question! In part 6.5 of "RNA-seqworkflow" working on cufflinks data. how should I change the ID conversion line? Should I leave it as it is or KEGG?

>...
Forum: Bioinformatics 06-21-2014, 05:33 AM
Replies: 15
Views: 12,397
Posted By Parharn
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...
Forum: Bioinformatics 06-20-2014, 01:59 AM
Replies: 15
Views: 12,397
Posted By Parharn
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...
Forum: Bioinformatics 06-19-2014, 03:14 PM
Replies: 15
Views: 12,397
Posted By Parharn
> 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...
Forum: Bioinformatics 06-19-2014, 12:48 PM
Replies: 15
Views: 12,397
Posted By Parharn
Ok, these are the outputs, where am I doing it...

Ok, these are the outputs, where am I doing it wrong?!

> lapply(kegg.gs[1:3], head, 3)
$`spo00970 Aminoacyl-tRNA biosynthesis`
[1] "SPAC17A5.15c" "SPAC1805.09c" "SPAC23A1.12c"

$`spo02010 ABC...
Forum: Bioinformatics 06-19-2014, 02:18 AM
Replies: 15
Views: 12,397
Posted By Parharn
Thanks for help, as I understood I should write...

Thanks for help, as I understood I should write the script as follow, which again I end up with the same error! I just copied anything in case you see something wrong in middle!

> require(gage)...
Forum: Bioinformatics 06-18-2014, 02:23 AM
Replies: 15
Views: 12,397
Posted By Parharn
Yes! I posted it in both forums since I need...

Yes! I posted it in both forums since I need help! Is it against rules or something?! Are seqanswers.com and biostars.org related somehow?!
Forum: Bioinformatics 06-18-2014, 01:21 AM
Replies: 15
Views: 12,397
Posted By Parharn
Parsing ./spoNA.xml file failed, please check the file!

I am trying the pathway analysis from this workflow (1). I recieve error that parsing some file failed! Other question I have is, if it is enough to just change the species="hsa" to species="spo" for...
Forum: Bioinformatics 06-17-2014, 03:03 PM
Replies: 2
Views: 1,703
Posted By Parharn
Yes I got help in another thread, you are right....

Yes I got help in another thread, you are right. Thanks a lot though.
Here is the other thread just if any one wanted to know more.
https://www.biostars.org/p/103482/#103584
Forum: Bioinformatics 06-16-2014, 04:46 AM
Replies: 2
Views: 1,703
Posted By Parharn
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
>...
Forum: Bioinformatics 06-11-2014, 10:46 AM
Replies: 3
Views: 1,758
Posted By Parharn
Thanks for the tips bigmw, I will give it a try...

Thanks for the tips bigmw, I will give it a try and see how it will goes.

Cheers,
/P
Showing results 1 to 25 of 84

 


All times are GMT -8. The time now is 01:34 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO