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Forum: Bioinformatics 01-03-2016, 11:18 PM
Replies: 20
Views: 9,533
Posted By areyes
Hi czelin, This is unlikely, since reads...

Hi czelin,

This is unlikely, since reads that overlap to many exons should be counted once per each exon. You could check whether the reads that are ignored by the script are properly paired or if...
Forum: Bioinformatics 01-07-2015, 03:15 AM
Replies: 9
Views: 2,941
Posted By areyes
Hi @shikha5, The error seems to be that a...

Hi @shikha5,

The error seems to be that a you have no replicates in your experiment.

As for the dataset with replication, could you add what Mike asked in post 6 and the error that you are...
Forum: Bioinformatics 12-03-2014, 07:19 AM
Replies: 5
Views: 988
Posted By areyes
Hi @unicornich, Sorry for the late reply....

Hi @unicornich,

Sorry for the late reply. How did the analysis go?

Are you expecting the treatment to cause a bias that is consistent for specific genes across replicates? Are you interested in...
Forum: Bioinformatics 12-02-2014, 03:27 AM
Replies: 3
Views: 1,237
Posted By areyes
I think I agree with you and I will fix this...

I think I agree with you and I will fix this issue! Thanks for noticing it!

Alejandro
Forum: Bioinformatics 12-02-2014, 12:35 AM
Replies: 3
Views: 1,237
Posted By areyes
Hi Neytiri, This sounds like a bug in the...

Hi Neytiri,

This sounds like a bug in the plotting function. Did you by chance modified the order of the results table? Could you send me a reproducible example to generate the plot that you...
Forum: Bioinformatics 11-18-2014, 05:01 AM
Replies: 9
Views: 5,323
Posted By areyes
Sorry for the very late reply. Could you confirm...

Sorry for the very late reply. Could you confirm if this happens when you have a moderate number of samples (around 10-12) and for genes with lots of exonic regions?

I think this has to do with...
Forum: Bioinformatics 09-24-2014, 12:15 AM
Replies: 4
Views: 1,809
Posted By areyes
Hi Marcus, You are right, so far one...

Hi Marcus,

You are right, so far one dispersion estimate is estimated for all the levels of the factorial designs.

I think that if you include the un-replicated cell-line when estimating the...
Forum: Bioinformatics 09-23-2014, 06:39 AM
Replies: 4
Views: 1,809
Posted By areyes
Dear Marcus, Of course the optimal is that...

Dear Marcus,

Of course the optimal is that you would have replicates for the third cell line. But what you could also try is to estimate the dispersions using only the cell lines for which you...
Forum: Bioinformatics 08-29-2014, 01:36 AM
Replies: 5
Views: 3,717
Posted By areyes
From old versions of DEXSeq, for instance: ...

From old versions of DEXSeq, for instance:

http://www.bioconductor.org/packages/2.12/bioc/html/DEXSeq.html

But I would rather add the NH flag, rather than using old, not-mantained software!
Forum: Bioinformatics 08-01-2014, 12:20 AM
Replies: 11
Views: 3,495
Posted By areyes
Hi finfin, the first messages that you are...

Hi finfin, the first messages that you are getting, are they warnings or errors?
When you changed the versions, you mention it is getting stuck in estimateDispersions, what version of DEXSeq are you...
Forum: Bioinformatics 06-20-2014, 05:47 AM
Replies: 9
Views: 5,323
Posted By areyes
you could try dropbox or similar tools!

you could try dropbox or similar tools!
Forum: Bioinformatics 06-17-2014, 04:22 AM
Replies: 9
Views: 5,323
Posted By areyes
Thanks for reporting this! The current...

Thanks for reporting this! The current implementation of DEXSeq estimates fold changes only for those exons for which a p-adjustes value was calculated (e.g. not being an outlier).

How many of...
Forum: RNA Sequencing 05-16-2014, 02:05 AM
Replies: 22
Views: 8,880
Posted By areyes
Hi @GreboGuru, I think that looks...

Hi @GreboGuru,

I think that looks reasonable, you would be testing for those cases where the treatment has a specific effect in exon usage in a specific time point.

Alejandro
Forum: Bioinformatics 05-09-2014, 07:16 AM
Replies: 15
Views: 4,591
Posted By areyes
I think STAR does looks for de novo junctions! ...

I think STAR does looks for de novo junctions!

Yes, the plot look funky! There seems to be three clouds of points, the lowest one is what is found in the "normal" cases. The upper clouds are the...
Forum: Bioinformatics 05-08-2014, 05:51 AM
Replies: 15
Views: 4,591
Posted By areyes
Hi all, I just saw a poster in a conference in...

Hi all, I just saw a poster in a conference in which they used the exon-exon junction counts from the STAR aligner as input to DEXSeq. It seemed to work nicely for human cancer genomes...
Forum: Bioinformatics 05-05-2014, 03:49 PM
Replies: 13
Views: 5,629
Posted By areyes
Hi Yohann, Thanks for reporting this! ...

Hi Yohann,

Thanks for reporting this!

I just committed DEXSeq version 1.10.1 to the release branch, the hang should be fixed there. You could either get it from the svn server right not or...
Forum: Bioinformatics 05-02-2014, 04:22 AM
Replies: 3
Views: 1,491
Posted By areyes
Hi @unicornich, If you ar using R-3.0.*,...

Hi @unicornich,

If you ar using R-3.0.*, have a look at this link,

https://stat.ethz.ch/pipermail/bioconductor/2014-April/059098.html

otherwise, could you include what @dpryan asked and the...
Forum: Introductions 04-23-2014, 11:25 PM
Replies: 18
Views: 3,822
Posted By areyes
Hi Mudita, "fitted expression" and "fitted...

Hi Mudita,

"fitted expression" and "fitted splicing" reflect the fitted values of the generalised linear model used by DEXSeq, you will find the details in the DEXSeq publication:
...
Forum: Bioinformatics 04-15-2014, 11:40 PM
Replies: 12
Views: 7,164
Posted By areyes
The perl version of @dpryan's script (be careful,...

The perl version of @dpryan's script (be careful, its perl!, :P)
Forum: Introductions 04-14-2014, 12:29 AM
Replies: 18
Views: 3,822
Posted By areyes
Hi Mudita, Thanks for providing the code and...

Hi Mudita,

Thanks for providing the code and the warnings! You have the answer in the warning:



Fast solution, try either changing the colors of the plot to ones without any transparency...
Forum: Introductions 04-13-2014, 11:26 PM
Replies: 18
Views: 3,822
Posted By areyes
Hi Mudita, Could you include the code that...

Hi Mudita,

Could you include the code that you are using and the output of sessionInfo()?
Are you getting an error or a warning?
Does it happen with all the genes?
Does it happen also when...
Forum: Bioinformatics 04-10-2014, 03:32 AM
Replies: 3
Views: 990
Posted By areyes
Hi Dorota, I had a similar problem trying to...

Hi Dorota,

I had a similar problem trying to do comparative transcriptomics of exon usage regulation in primate species. I can give some input that I hope could be useful for you, but first let...
Forum: Bioinformatics 04-09-2014, 08:57 AM
Replies: 4
Views: 4,446
Posted By areyes
Hi @TheSeqGeek, You have to use the adjusted...

Hi @TheSeqGeek,

You have to use the adjusted p-values.

Everytime you do multiple tests (not only with RNA-seq data), you need to correct for what you would expect to be significant just by...
Forum: RNA Sequencing 04-01-2014, 11:44 PM
Replies: 6
Views: 3,864
Posted By areyes
Hi kajot, I have the feeling that could be...

Hi kajot,

I have the feeling that could be related to the protocol that you are using. In the most recent protocol of the illumina runs (at least the latest used by the sequencing facility at...
Forum: Introductions 03-28-2014, 12:24 AM
Replies: 18
Views: 3,822
Posted By areyes
Hi Mudita, Are you getting an error message?...

Hi Mudita,

Are you getting an error message? I would almost bet that you are getting this error:

"Error in testForDEU: argument 2 matches multiple formal arguments"

You have to change your...
Showing results 1 to 25 of 165

 


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