Forum: Bioinformatics
05-19-2019, 11:57 AM
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Replies: 1
Views: 4,104
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Forum: Bioinformatics
02-18-2016, 11:32 AM
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Replies: 5
Views: 1,569
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Forum: Bioinformatics
01-02-2016, 11:37 PM
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Replies: 2
Views: 2,176
Have you tried the ggbio package?...
Have you tried the ggbio package? http://www.tengfei.name/ggbio/ -- see also the gallery there, or do a google image search with 'ggbio' to look for example plots.
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Forum: Bioinformatics
12-29-2014, 06:23 AM
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Replies: 4
Views: 2,631
Habbas
are you using the most recent...
Habbas
are you using the most recent versions of R and the packages?
See http://www.bioconductor.org/packages/release/bioc/html/GenomicAlignments.html (version 1.2.1) and in fact I would even try...
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Forum: Bioinformatics
12-23-2014, 12:56 AM
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Replies: 10
Views: 6,632
Dear Keysoon
I suggest investigating the...
Dear Keysoon
I suggest investigating the results and the input data for those genes that (i) only edgeR finds, (ii) only DESeq2 finds, (iii) both find.
Devon's hypothesis is pertinent. In...
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Forum: Bioinformatics
12-22-2014, 07:29 AM
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Replies: 2
Views: 2,405
Dear AGGP11,
there is no fundamental reason...
Dear AGGP11,
there is no fundamental reason why DESeq2 should not work with data from such an approach. As you say, the crucial assumption is that the number of reads for a gene is (to good enough...
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Forum: Bioinformatics
12-17-2014, 11:13 AM
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Replies: 4
Views: 2,633
Dear Hannah
Have a look at this posting guide:...
Dear Hannah
Have a look at this posting guide: http://www.bioconductor.org/help/support/posting-guide for suggestions how to ask questions in a way that permit others to give a useful answer (esp....
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Forum: Bioinformatics
11-07-2014, 11:12 PM
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Replies: 1
Views: 1,530
Dear Surjray
it may be difficult to help you...
Dear Surjray
it may be difficult to help you based on the information provided. Can you post a self-contained code example (with example data, e.g. you could use the 'pasilla' package) that...
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Forum: Bioinformatics
10-12-2014, 06:43 AM
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Replies: 0
Views: 1,430
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Forum: Bioinformatics
08-10-2014, 12:40 AM
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Replies: 2
Views: 2,655
Filtering out likely uninformative variables...
Filtering out likely uninformative variables (e.g. with low overall variance after rlog or VST) can also improve clustering. As in the best case, they only add noise and uniformly increase all...
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Forum: Bioinformatics
08-04-2014, 09:43 AM
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Replies: 9
Views: 13,708
Note that something is missing in what you...
Note that something is missing in what you describe: if the lowest count in your cases is really 20000 and the highest in your controls 200, then that's a fold change of over 100, or >6.5 on the log2...
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Forum: Bioinformatics
08-04-2014, 01:26 AM
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Replies: 9
Views: 13,708
Dear ExMachina
Have a look at the...
Dear ExMachina
Have a look at the documentation of the package, i.e. the vignette or the man page of the results function. There it says:
By default, independent filtering is performed to...
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Forum: Bioinformatics
05-09-2014, 11:35 AM
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Replies: 1
Views: 2,580
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Forum: Bioinformatics
04-30-2014, 11:14 AM
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Replies: 8
Views: 10,796
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Forum: Bioinformatics
04-30-2014, 11:11 AM
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Replies: 8
Views: 10,796
Yes. And depending on the data, there may not...
Yes. And depending on the data, there may not always be a variance stabilising transformation. In particular, the error model on which the transformation is based assumes that for most genes the...
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Forum: Bioinformatics
04-30-2014, 11:01 AM
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Replies: 1
Views: 1,780
Dear Ayana
the DESeq package is still...
Dear Ayana
the DESeq package is still supported including the getVarianceStabilizedData function etc. It is not clear what you mean by 'dysfunctional'? If you have a problem, can you please post a...
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Forum: Bioinformatics
04-26-2014, 03:05 AM
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Replies: 1
Views: 1,534
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Forum: Bioinformatics
03-06-2014, 10:26 AM
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Replies: 12
Views: 10,178
Dear Luise
my advice here would be to put...
Dear Luise
my advice here would be to put less emphasis on the testing (your point 1.) and move straight to point 2. (clustering), using one of the transformations described in the DESeq2 vignette...
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Forum: Bioinformatics
02-20-2014, 06:13 AM
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Replies: 6
Views: 2,583
Olga, Mariana
sorry for not responding...
Olga, Mariana
sorry for not responding earlier, not sure why this slipped through (it might also be useful to ask questions about Bioconductor packages on the Bioconductor mailing list...
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Forum: Bioinformatics
01-24-2014, 01:37 PM
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Replies: 4
Views: 2,043
Hi ccard28
you need to make sure that your...
Hi ccard28
you need to make sure that your 'countTable' is a data.frame whose columns are numeric variables of storage class 'integer', and contain no NA (and no negative) values. It might be...
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Forum: Bioinformatics
01-19-2014, 11:59 AM
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Replies: 6
Views: 2,459
Dear PhD1990
it's good that you report...
Dear PhD1990
it's good that you report having a problem. Probably you need to be more specific for someone to be able to help you. Can you provide a
- reproducible example (i.e. a...
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Forum: Bioinformatics
12-26-2013, 12:06 AM
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Replies: 2
Views: 1,937
Dear Giu.facchetti,
thank you for the...
Dear Giu.facchetti,
thank you for the feedback. Some suggestions:
1. The attached jpeg image came out very small (100x115x) making it hard to impossible to read (at least for me).
2. Such a...
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Forum: Bioinformatics
09-07-2013, 03:47 PM
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Replies: 1
Views: 3,215
Dear Narges
simulation is great to check how...
Dear Narges
simulation is great to check how well your software does (or approximates) what your theory says, but it does not help with the question whether your theory (or: model) agrees with...
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Forum: Bioinformatics
08-26-2013, 11:56 PM
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Replies: 4
Views: 3,487
Dear mbk0asis
this is really an R question,...
Dear mbk0asis
this is really an R question, nothing specific to DESeq. At the most basic level, have a look at the functions text, identify and locate in R's default graphics package. Then,
...
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Forum: Bioinformatics
08-25-2013, 06:57 AM
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Replies: 9
Views: 19,106
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