Forum: Bioinformatics
01-03-2016, 11:18 PM
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Replies: 20
Views: 12,000
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...
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Forum: Bioinformatics
01-07-2015, 03:15 AM
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Replies: 9
Views: 3,839
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...
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Forum: Bioinformatics
12-03-2014, 07:19 AM
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Replies: 5
Views: 1,485
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...
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Forum: Bioinformatics
12-02-2014, 03:27 AM
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Replies: 3
Views: 1,744
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Forum: Bioinformatics
12-02-2014, 12:35 AM
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Replies: 3
Views: 1,744
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...
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Forum: Bioinformatics
11-18-2014, 05:01 AM
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Replies: 9
Views: 6,830
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Forum: Bioinformatics
09-24-2014, 12:15 AM
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Replies: 4
Views: 2,454
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...
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Forum: Bioinformatics
09-23-2014, 06:39 AM
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Replies: 4
Views: 2,454
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...
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Forum: Bioinformatics
08-29-2014, 01:36 AM
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Replies: 5
Views: 4,897
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!
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Forum: Bioinformatics
08-01-2014, 12:20 AM
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Replies: 11
Views: 4,602
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...
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Forum: Bioinformatics
06-20-2014, 05:47 AM
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Replies: 9
Views: 6,830
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Forum: Bioinformatics
06-17-2014, 04:22 AM
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Replies: 9
Views: 6,830
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...
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Forum: RNA Sequencing
05-16-2014, 02:05 AM
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Replies: 22
Views: 12,576
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
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Forum: Bioinformatics
05-09-2014, 07:16 AM
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Replies: 15
Views: 5,869
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Forum: Bioinformatics
05-08-2014, 05:51 AM
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Replies: 15
Views: 5,869
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Forum: Bioinformatics
05-05-2014, 03:49 PM
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Replies: 13
Views: 7,611
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...
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Forum: Bioinformatics
05-02-2014, 04:22 AM
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Replies: 3
Views: 2,069
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...
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Forum: Introductions
04-23-2014, 11:25 PM
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Replies: 18
Views: 4,979
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:
...
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Forum: Bioinformatics
04-15-2014, 11:40 PM
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Replies: 12
Views: 9,557
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Forum: Introductions
04-14-2014, 12:29 AM
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Replies: 18
Views: 4,979
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...
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Forum: Introductions
04-13-2014, 11:26 PM
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Replies: 18
Views: 4,979
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...
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Forum: Bioinformatics
04-10-2014, 03:32 AM
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Replies: 3
Views: 1,394
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...
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Forum: Bioinformatics
04-09-2014, 08:57 AM
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Replies: 4
Views: 6,561
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...
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Forum: RNA Sequencing
04-01-2014, 11:44 PM
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Replies: 6
Views: 5,207
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...
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Forum: Introductions
03-28-2014, 12:24 AM
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Replies: 18
Views: 4,979
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...
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