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Search: Posts Made By: Wolfgang Huber
Forum: Bioinformatics 05-19-2019, 11:57 AM
Replies: 1
Views: 670
Posted By Wolfgang Huber
Hi Nicolas Assertions 2-4 seem OK, but 1 is...

Hi Nicolas

Assertions 2-4 seem OK, but 1 is not correct. The best I could come up with to explain this is in the recent book:...
Forum: Bioinformatics 02-18-2016, 11:32 AM
Replies: 5
Views: 869
Posted By Wolfgang Huber
The original post was cross-posted, and is...

The original post was cross-posted, and is answered here: https://support.bioconductor.org/p/78427/#78550
Forum: Bioinformatics 01-02-2016, 11:37 PM
Replies: 2
Views: 1,375
Posted By Wolfgang Huber
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.
Forum: Bioinformatics 12-29-2014, 06:23 AM
Replies: 4
Views: 1,784
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 12-23-2014, 12:56 AM
Replies: 10
Views: 4,892
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 12-22-2014, 07:29 AM
Replies: 2
Views: 1,684
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 12-17-2014, 11:13 AM
Replies: 4
Views: 1,672
Posted By Wolfgang Huber
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....
Forum: Bioinformatics 11-07-2014, 11:12 PM
Replies: 1
Views: 996
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 10-12-2014, 06:43 AM
Replies: 0
Views: 855
Posted By Wolfgang Huber
Advanced Course: R programming and development 15-16. January 2015 (Thursday-Friday)

See here for primary course announcement and registration. (http://www.dataprogrammers.net/embl_jan2015/)

This course is designed for users who have experience with writing R scripts, and who now...
Forum: Bioinformatics 08-10-2014, 12:40 AM
Replies: 2
Views: 1,778
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 08-04-2014, 09:43 AM
Replies: 9
Views: 8,386
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 08-04-2014, 01:26 AM
Replies: 9
Views: 8,386
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 05-09-2014, 11:35 AM
Replies: 1
Views: 1,732
Posted By Wolfgang Huber
Dear Yohann thanks for the feedback. All of...

Dear Yohann

thanks for the feedback. All of that behaviour is intended, and the rationale behind it is described in the DEXSeq Paper...
Forum: Bioinformatics 04-30-2014, 11:14 AM
Replies: 8
Views: 8,998
Posted By Wolfgang Huber
@Him26: Note that in John's plots the y-axis is...

@Him26: Note that in John's plots the y-axis is on a log-scale.
If you do the same kind of plot with sd computed on the original scale of the counts, then you will indeed expect them to increase...
Forum: Bioinformatics 04-30-2014, 11:11 AM
Replies: 8
Views: 8,998
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 04-30-2014, 11:01 AM
Replies: 1
Views: 1,209
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 04-26-2014, 03:05 AM
Replies: 1
Views: 1,059
Posted By Wolfgang Huber
See the thread on the Bioconductor list,...

See the thread on the Bioconductor list, http://comments.gmane.org/gmane.science.biology.informatics.conductor/54591 (cross-post)
Forum: Bioinformatics 03-06-2014, 10:26 AM
Replies: 12
Views: 7,857
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 02-20-2014, 06:13 AM
Replies: 6
Views: 1,938
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 01-24-2014, 01:37 PM
Replies: 4
Views: 1,517
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 01-19-2014, 11:59 AM
Replies: 6
Views: 1,693
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 12-26-2013, 12:06 AM
Replies: 2
Views: 1,433
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 09-07-2013, 03:47 PM
Replies: 1
Views: 2,628
Posted By Wolfgang Huber
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...
Forum: Bioinformatics 08-26-2013, 11:56 PM
Replies: 4
Views: 2,704
Posted By Wolfgang Huber
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,

...
Forum: Bioinformatics 08-25-2013, 06:57 AM
Replies: 9
Views: 10,401
Posted By Wolfgang Huber
Dear N. try removing either one of the...

Dear N.

try removing either one of the columns "Sample" or "Replicate", it seems they are redundant of each other.

Best wishes
Wolfgang
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