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Forum: RNA Sequencing 06-06-2012, 12:45 PM
Replies: 8
Views: 2,281
Posted By chknbio
I have a similar question. I would like to know...

I have a similar question. I would like to know if there is differential expression of unannotated transcripts in RNAseq data. I have a particular unannotated transcript that I can see visually as...
Forum: Bioinformatics 05-29-2012, 02:00 PM
Replies: 2
Views: 1,501
Posted By chknbio
It looks like I have everything installed except...

It looks like I have everything installed except XML which is preventing other packages from installing. But when I look at linux system, XML is installed. How can I get it to work in R so that I...
Forum: Bioinformatics 05-29-2012, 01:18 PM
Replies: 2
Views: 2,653
Posted By chknbio
I am also having a problem installing goseq. ...

I am also having a problem installing goseq.


Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package XML had non-zero exit status
2:...
Forum: Bioinformatics 05-29-2012, 01:15 PM
Replies: 2
Views: 1,501
Posted By chknbio
This is the message that I receive when trying to...

This is the message that I receive when trying to run goseq:


Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package XML had non-zero...
Forum: Bioinformatics 05-29-2012, 01:10 PM
Replies: 2
Views: 1,501
Posted By chknbio
installing goseq

I am trying to install goseq in R, but receiving installation errors. It looks like other packages are missing when I try to install those other packages I get install errors too, which also suggest...
Forum: Bioinformatics 05-25-2012, 11:55 AM
Replies: 5
Views: 3,138
Posted By chknbio
Ingenuity looks like a great product for RNAseq...

Ingenuity looks like a great product for RNAseq pathway analysis but does any similar open course (free) program exist which provides similar analysis results?

Thanks.
Forum: Bioinformatics 05-25-2012, 11:53 AM
Replies: 22
Views: 4,733
Posted By chknbio
I have a list of DE genes in chicken tumor...

I have a list of DE genes in chicken tumor samples retrieved from a cuffdiff analysis. I would like to determine if these genes are part of a pathway. Does anyone have a recommendation for a...
Forum: RNA Sequencing 05-25-2012, 11:50 AM
Replies: 12
Views: 8,598
Posted By chknbio
I am working with chicken RNAseq dataset. I...

I am working with chicken RNAseq dataset. I completed my analysis with cuffdiff and have a list of DE genes. How can I do about finding if these genes are involved in a pathway? Can I use the...
Forum: Bioinformatics 05-24-2012, 12:20 PM
Replies: 8
Views: 3,779
Posted By chknbio
This is helpful. Thank you!

This is helpful. Thank you!
Forum: Bioinformatics 05-24-2012, 10:56 AM
Replies: 8
Views: 3,779
Posted By chknbio
This is a very good tutorial here, but it still...

This is a very good tutorial here, but it still leaves some questions unanswered.
http://vallandingham.me/RNA_seq_differential_expression.html

How do you determine what cuffdiff lists as...
Forum: RNA Sequencing 05-24-2012, 10:07 AM
Replies: 1
Views: 1,317
Posted By chknbio
I am also looking for an answer to (d) listed in...

I am also looking for an answer to (d) listed in your post. Did you find an answer to this question? Or does anyone have an answer to how to you determine, output the genes that are upregulated or...
Forum: Bioinformatics 05-24-2012, 09:50 AM
Replies: 8
Views: 3,779
Posted By chknbio
Hi Bjorn, Thank you for the reply. And for...

Hi Bjorn,

Thank you for the reply. And for the link on this tool. I already have the cuffdiff output and I would use command line but I am wondering where to begin. How do I retrieve all of the...
Forum: Bioinformatics 05-24-2012, 09:37 AM
Replies: 8
Views: 3,779
Posted By chknbio
yes, I have used cummeRbund to plot some of the...

yes, I have used cummeRbund to plot some of the graphs. Which look nice, but I am more curious in pulling out differential expressed genes. I would like to look at the data globally vs. picking and...
Forum: Bioinformatics 05-24-2012, 08:45 AM
Replies: 8
Views: 3,779
Posted By chknbio
RNAseq data analysis

I recently started some RNAsequencing of tumor samples. My main question is regarding the differential gene expression among samples and controls. I have successful utilized tophat, cufflinks, and...
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