SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 28
Search took 0.00 seconds.
Search: Posts Made By: rory
Forum: Bioinformatics 05-05-2016, 08:22 AM
Replies: 6
Views: 1,166
Posted By rory
This has generated a lot of discussion recently....

This has generated a lot of discussion recently. Subtracting the reads, as DiffBind does by default, is a bit of a kludge that potentially violates the assumptions of the statistics underlying the...
Forum: Bioinformatics 05-05-2016, 07:01 AM
Replies: 6
Views: 1,166
Posted By rory
There isn't a way to prevent the underlying...

There isn't a way to prevent the underlying differential analysis method from normalizing the read counts. The score parameter only changes the scoring method used for plots of global (non-analyzed)...
Forum: Bioinformatics 04-18-2016, 07:32 AM
Replies: 1
Views: 746
Posted By rory
If you have replicates, the Bioconductor package...

If you have replicates, the Bioconductor package DiffBind does exactly this kind of analysis. There is a vignette that shows all the steps with example data.

If you do not have replicates, you...
Forum: Bioinformatics 10-29-2015, 08:25 AM
Replies: 10
Views: 4,136
Posted By rory
Try: >...

Try:

> samples<-dba(sampleSheet="samples.csv", scoreCol=0)

This tells DiffBind that there are no scores. Note that everything will get an identical score of 1, so clustering/PCA plots won't be...
Forum: Bioinformatics 09-23-2015, 02:05 AM
Replies: 3
Views: 1,970
Posted By rory
If you could re-post this issue to the...

If you could re-post this issue to the Bioconductor support site:
https://support.bioconductor.org/'

we can address this there. Please do include the sessionInfo() output.

The way you are...
Forum: Bioinformatics 01-06-2015, 06:40 AM
Replies: 2
Views: 1,550
Posted By rory
I can offer some instructions on using DiffBind,...

I can offer some instructions on using DiffBind, but MACS2 may not be your best choice for broad histone marks. There are a number of other options out there (we use SICER). You may also want to look...
Forum: Bioinformatics 12-17-2014, 03:44 AM
Replies: 8
Views: 3,867
Posted By rory
This page, "ENCODE: TF ChIP-seq peak calling...

This page, "ENCODE: TF ChIP-seq peak calling using the Irreproducibility Discovery Rate (IDR) framework" (https://sites.google.com/site/anshulkundaje/projects/idr) , contains the instructions...
Forum: Bioinformatics 12-10-2014, 06:01 AM
Replies: 8
Views: 3,867
Posted By rory
I'll ChIP in on this one... In general, it...

I'll ChIP in on this one...

In general, it is not a good idea to combine the reads from biological replicates. One reason is that you lose the ability to distinguish the biological and...
Forum: Bioinformatics 10-20-2014, 10:09 AM
Replies: 5
Views: 3,032
Posted By rory
The easiest way to read MACS peaks into DiffBind...

The easiest way to read MACS peaks into DiffBind is to specify the .xls files in the sample sheet and specify "macs" as the peak caller (either in a column of the sample sheet, or using the...
Forum: Bioinformatics 09-09-2014, 12:03 PM
Replies: 6
Views: 2,072
Posted By rory
It appears that DiffBind can't handle the "-"...

It appears that DiffBind can't handle the "-" character (minus sign/hyphen) in the file names. Remove them and it should work!

Cheers-
Rory
Forum: Bioinformatics 07-18-2014, 05:18 AM
Replies: 1
Views: 675
Posted By rory
The ChIPQC package...

The ChIPQC package (http://bioconductor.org/packages/release/bioc/html/ChIPQC.html) in Bioconductor (http://bioconductor.org/) will show how all your ChIPs compare. It was designed specifically for...
Forum: Bioinformatics 04-16-2014, 09:25 AM
Replies: 2
Views: 1,617
Posted By rory
Post ChIPQC: a package for assessing quality of ChIP-seq samples and experiments

In conjunction with my colleague, Thomas Carroll, who has been looking at quality metrics for ChIP-seq libraries on a large scale (including evaluating more than 400 ENCODE libraries), we have...
Forum: Bioinformatics 03-26-2014, 02:48 AM
Replies: 3
Views: 1,184
Posted By rory
There's also the Rcade ...

There's also the Rcade (http://bioconductor.org/packages/release/bioc/html/Rcade.html) package in Bioconductor (R-based analysis of ChIP-seq And Differential Expression)...
Forum: Bioinformatics 12-03-2013, 05:06 AM
Replies: 1
Views: 1,847
Posted By rory
This depends on whether you are looking to do de...

This depends on whether you are looking to do de novo motif discovery or are looking for enrichment of known motifs. We find that the latter is generally more useful for the types of questions we are...
Forum: Academic/Non-Profit Jobs 05-31-2013, 11:25 AM
Replies: 1
Views: 2,218
Posted By rory
For those interested, the closing date for...

For those interested, the closing date for applications is 12 June.
Forum: Bioinformatics 05-31-2013, 05:06 AM
Replies: 26
Views: 2,954
Posted By rory
If you are getting pushback, you can point them...

If you are getting pushback, you can point them at this concise, pithy paper:

Hansen KD, Wu Z, Irizarry RA, Leek JT. "Sequencing technology does not eliminate biological variability." Nature...
Forum: Academic/Non-Profit Jobs 05-15-2013, 04:29 AM
Replies: 1
Views: 2,218
Posted By rory
Senior Bioinformatics Analyst - University of Cambridge/Cancer Research UK

For those who may be interested, we are hiring for a senior analyst position. Feel free to write to me directly if you have any questions about the role.

http://www.jobs.cam.ac.uk/job/1484/
...
Forum: Bioinformatics 04-13-2013, 06:52 AM
Replies: 4
Views: 2,008
Posted By rory
The Bioconductor package DiffBind makes this very...

The Bioconductor package DiffBind makes this very easy, have a look at the vignette.
Forum: Bioinformatics 04-08-2013, 04:30 AM
Replies: 14
Views: 3,741
Posted By rory
This is a very good question, and while it does...

This is a very good question, and while it does not yet have a definitive answer, there is literature suggesting that differentially bound sites have biological significance.

For example, we have...
Forum: Bioinformatics 04-08-2013, 04:07 AM
Replies: 14
Views: 3,741
Posted By rory
Here's my understanding of why we need...

Here's my understanding of why we need replicates:

There is substantial variance in read density at specific peak sites between biological and technical replicates. Without replicating the...
Forum: Bioinformatics 04-08-2013, 03:40 AM
Replies: 14
Views: 3,741
Posted By rory
The Bioconductor package DiffBind has a number of...

The Bioconductor package DiffBind has a number of normalization options, with the default using the edgeR TMM (based on effective library size after subtracting control reads). It makes it easy to do...
Forum: Bioinformatics 02-21-2013, 02:47 AM
Replies: 10
Views: 4,136
Posted By rory
Another tool to try is the Bioconductor package...

Another tool to try is the Bioconductor package DiffBind:
http://www.bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf

It gives you a number of ways to compare...
Forum: Bioinformatics 10-23-2012, 04:07 AM
Replies: 2
Views: 2,498
Posted By rory
Here's how I'd interpret these phrases: TF...

Here's how I'd interpret these phrases:

TF binding site: specific location on the genome where a TF binds. In the canonical scenario, this would be the where the binding motif is located.

TF...
Forum: Bioinformatics 07-03-2012, 03:48 AM
Replies: 1
Views: 2,021
Posted By rory
The real comparison of interest is not between...

The real comparison of interest is not between coverage of bound sites vs. coverage of the control, but rather having comparable sequencing depth between the ChIP background and the control.

"In...
Forum: Bioinformatics 05-30-2012, 03:58 AM
Replies: 5
Views: 3,032
Posted By rory
We have analyzed MeDIP both using peak callers...

We have analyzed MeDIP both using peak callers (MACS) and pre-defined regions (promoters, 3'UTR, introns, etc.). In any case, we keep the replicates separate, deriving different peaksets for each...
Showing results 1 to 25 of 28

 


All times are GMT -8. The time now is 10:35 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO