Moderator: Wolfgang Huber

gravatar for Wolfgang Huber
Reputation:
12,950
Status:
Trusted
Location:
EMBL European Molecular Biology Laboratory
Website:
http://www.embl.de/res...
Scholar ID:
Google Scholar Page
Last seen:
2 weeks ago
Joined:
16 years, 4 months ago
Email:
w*****@embl.de

Posts by Wolfgang Huber

<prev • 1,367 results • page 2 of 137 • next >
0
votes
0
answers
376
views
0
answers
Comment: C: Conversion to SingleCellExperiment from Seurat objects
... See also https://github.com/satijalab/seurat/issues/485 and https://github.com/satijalab/seurat/pull/487 ...
written 5 months ago by Wolfgang Huber13k
0
votes
0
answers
376
views
0
answers
Conversion to SingleCellExperiment from Seurat objects
... I realize this is slightly out of scope since Seurat 2.3 is on CRAN, not Bioconductor, but given its developers recent interactions with the SIngleCellExperiment developers, I hope it's OK to post this here:   When trying to convert one of the Seurat data objects from the tabula muris, I get the f ...
seurat singlecellexperiment written 5 months ago by Wolfgang Huber13k
8
votes
0
answers
239
views
0
answers
exprs function - clash with dplyr
... I wanted to highlight a recent1 change in the dplyr package that is likely to break a lot of people's existing code. That package now exports2 a function named exprs, which masks a function of the same name from the Biobase package. The latter tends to be used frequently in conjunction with Expr ...
biobase dplyr exprs written 5 months ago by Wolfgang Huber13k
0
votes
1
answers
119
views
1
answers
Comment: C: Stacked density plots not working in for loop (graphical device crashing?)
... Hmm, please consider that people are more likely to be able to give a meaningful response if you followed the posting guide and did your homework. In particular, can you please try with the up-to-date version of R and install up-to-date versions of all required packages  from scratch? can you pr ...
written 5 months ago by Wolfgang Huber13k
0
votes
2
answers
372
views
2
answers
Answer: A: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
... Interesting thread and good discussion. I'd like to make two additional remarks: 1.) Aaron said (emphases from me) "The log-transformation provides some measure of variance stabilisation for count data, with the added bonus that differences between log-values directly represent log-fold changes (wh ...
written 5 months ago by Wolfgang Huber13k
0
votes
2
answers
231
views
2
answers
Answer: A: Limma - how to manage huge differences in library sizes
... Is this a data quality problem or an expected consequence of the experimental design? If it's the former, then perhaps it's best to stop here. If it's the latter, then what is your approach to deconfound true biological effects on library size from technical variations? Do you have spike-in contro ...
written 5 months ago by Wolfgang Huber13k
0
votes
1
answers
164
views
1
answers
Answer: A: How to Remove EBImage objects that have holes?
... There are probably better ways, but how about this: library("EBImage") x = readImage(system.file(file.path("images", "nuclei.tif"), package = "EBImage"), all = FALSE) y = thresh(x, w = 15, h = 15, offset = 0.1) yf = fillHull(y) objects = bwlabel(yf) owh = unique(objects[ y != fillHull(y) ]) obje ...
written 6 months ago by Wolfgang Huber13k
0
votes
2
answers
202
views
2
answers
Answer: A: Is there a data package containing complex RNA-Seq data?
... Have a look at https://jhubiostatistics.shinyapps.io/recount/ ...
written 7 months ago by Wolfgang Huber13k
0
votes
2
answers
184
views
2
answers
Answer: A: Errors of loading HilbertVisGUI
... Have you tried the suggestion given by the error message?   P.S.: Please also have a look at the posting guide and try to post your questions following it: https://www.bioconductor.org/help/support/posting-guide/ ...
written 8 months ago by Wolfgang Huber13k
0
votes
1
answers
279
views
1
answers
Comment: C: rlog transformation producing outliers with very high log-transformed counts
... Two more points: Data quality: If the size factors (or indeed the library sizes) vary strongly across what should be comparable assays, is this perhaps a quality issue, meaning that some of the (presumably very low coverage) samples should be ignored rather than making a pretense of analysing the ...
written 8 months ago by Wolfgang Huber13k

Latest awards to Wolfgang Huber

Appreciated 4 months ago, created a post with more than 5 votes. For exprs function - clash with dplyr
Popular Question 4 months ago, created a question with more than 1,000 views. For European Bioconductor Developers' Meeting 12th-13th January 2015, Heidelberg
Scholar 4 months ago, created an answer that has been accepted. For A: Using DESeq2 normalisation method on a tximport list of matrices without sample
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Student 5 months ago, asked a question with at least 3 up-votes. For exprs function - clash with dplyr
Popular Question 5 months ago, created a question with more than 1,000 views. For DESeq2
Scholar 5 months ago, created an answer that has been accepted. For A: Using DESeq2 normalisation method on a tximport list of matrices without sample
Guru 16 months ago, received more than 100 upvotes.
Appreciated 16 months ago, created a post with more than 5 votes. For BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
Popular Question 16 months ago, created a question with more than 1,000 views. For DESeq2
Scholar 16 months ago, created an answer that has been accepted. For A: Nonspecific filtering of microarray data
Popular Question 19 months ago, created a question with more than 1,000 views. For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Popular Question 19 months ago, created a question with more than 1,000 views. For DESeq2
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 20 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Voter 2.5 years ago, voted more than 100 times.
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Processing imaging data from high throughput compound screen with EBImage
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 2.5 years ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 2.5 years ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 2.5 years ago, created an answer that has been accepted. For A: How is the mean-variance plot calculated?
Scholar 2.5 years ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 143 users visited in the last hour