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Forum: Bioinformatics 03-18-2014, 01:27 AM
Replies: 92
Views: 38,233
Posted By shocker8786
Thank you very much for that explanation, this is...

Thank you very much for that explanation, this is starting to make more sense to me now. I will make the necessary changes and retry. Thanks again!
Forum: Bioinformatics 03-17-2014, 02:11 AM
Replies: 92
Views: 38,233
Posted By shocker8786
I retried the code and was still not successful...

I retried the code and was still not successful with one of my datasets. I am sure that the code I am using is the same for both datasets (I have been copying and pasting the code for both datasets)....
Forum: Bioinformatics 03-15-2014, 05:17 AM
Replies: 92
Views: 38,233
Posted By shocker8786
Thank you for your help. I have 2 data sets that...

Thank you for your help. I have 2 data sets that I am trying to perform this analysis on (all pig), and I was indeed able to produce the results files as expected by changing those lines of code for...
Forum: Bioinformatics 03-14-2014, 01:29 AM
Replies: 92
Views: 38,233
Posted By shocker8786
I think you are right, but I'm not sure how...

I think you are right, but I'm not sure how exactly to download the pathway data files. I thought the step you told me to change (below) would download the package I need, but it fails:
...
Forum: Bioinformatics 03-13-2014, 01:26 AM
Replies: 92
Views: 38,233
Posted By shocker8786
Thanks for your reply, and for informing me about...

Thanks for your reply, and for informing me about the org="Ss" command. Unfortunately I am still unable to make it through the workflow without error. Below is my code and final output. Do you see...
Forum: Bioinformatics 03-12-2014, 07:32 AM
Replies: 92
Views: 38,233
Posted By shocker8786
changing range(exp.fc) to range(cuff.fc) results...

changing range(exp.fc) to range(cuff.fc) results in the following result printed by R:
[1] -Inf Inf

So is this a typo in the RNAseq workflow, or am I already supposed to have exp.fc defined? I'm...
Forum: Bioinformatics 03-12-2014, 07:02 AM
Replies: 92
Views: 38,233
Posted By shocker8786
I have a question about using GAGE with data from...

I have a question about using GAGE with data from cufflinks, as described in the RNA-Seq workflow tutorial. I have RNAseq data from pigs that was aligned using Tophat and analyzed for DEGs using...
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