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Forum: Bioinformatics 10-11-2011, 10:30 AM
Replies: 6
Views: 5,999
Posted By ecofriendly
Hi everyone, Here's a technical question....

Hi everyone,

Here's a technical question. I'm trying to use the newest version of DESeq (1.5.24, found here: http://bioconductor.org/packages/devel/bioc/html/DESeq.html), because it would enable...
Forum: Bioinformatics 08-26-2011, 11:54 AM
Replies: 31
Views: 12,661
Posted By ecofriendly
Quick question about Cuffdiff: Can it handle a...

Quick question about Cuffdiff: Can it handle a time course in which each time point is compared back to the same reference point?

I am doing a complicated time series of various treatments in...
Forum: Bioinformatics 05-04-2011, 10:42 AM
Replies: 34
Views: 36,155
Posted By ecofriendly
Not sure if the attachment went through...trying...

Not sure if the attachment went through...trying again
Forum: Bioinformatics 05-04-2011, 10:38 AM
Replies: 34
Views: 36,155
Posted By ecofriendly
Hi Simon, Please see the attachment.

Hi Simon, Please see the attachment.
Forum: Bioinformatics 05-04-2011, 09:06 AM
Replies: 34
Views: 36,155
Posted By ecofriendly
Dear Simon, First of all, thanks for your...

Dear Simon,

First of all, thanks for your response and clarification. I see your point regarding Fig. 3 in the paper, which is consistent with my own MvA plots - that at low expression levels,...
Forum: Bioinformatics 05-03-2011, 09:25 AM
Replies: 34
Views: 36,155
Posted By ecofriendly
I have a question for Simon and others regarding...

I have a question for Simon and others regarding how to use shot noise when interpreting the DESeq output, i.e. differentially expressed genes within a given p-value cutoff.

It seems that Figure 1...
Forum: Bioinformatics 11-27-2010, 08:24 PM
Replies: 3
Views: 3,548
Posted By ecofriendly
hello, This is a great forum and I'm...

hello,

This is a great forum and I'm learning a lot here. I would really appreciate some help troubleshooting HTSeq.

I've installed everything correctly in the Python window, I think, since I...
Forum: RNA Sequencing 11-24-2010, 01:31 PM
Replies: 15
Views: 23,469
Posted By ecofriendly
mrawlins, can you suggest an article that...

mrawlins, can you suggest an article that explains the difference between these different statistical tests and why they require different numbers of biological replicates of RNA-seq data to be as...
Forum: Introductions 11-23-2010, 08:19 AM
Replies: 373
Views: 150,920
Posted By ecofriendly
hi all, I'm new to this forum, but it seems...

hi all,
I'm new to this forum, but it seems like a great place to find information relating to RNA-seq. Currently, I'm a PhD student using methods like Illumina sequencing of mRNAs to study cell...
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