Moderator: Wolfgang Huber

gravatar for Wolfgang Huber
Reputation:
12,920
Status:
Trusted
Location:
EMBL European Molecular Biology Laboratory
Website:
http://www.embl.de/res...
Scholar ID:
Google Scholar Page
Last seen:
1 week ago
Joined:
16 years, 1 month ago
Email:
w*****@embl.de

Posts by Wolfgang Huber

<prev • 1,365 results • page 2 of 137 • next >
8
votes
0
answers
174
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 8 weeks ago by Wolfgang Huber13k
0
votes
1
answers
81
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 9 weeks ago by Wolfgang Huber13k
0
votes
2
answers
238
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 9 weeks ago by Wolfgang Huber13k
0
votes
2
answers
157
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 10 weeks ago by Wolfgang Huber13k
0
votes
1
answers
115
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 3 months ago by Wolfgang Huber13k
0
votes
2
answers
154
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 4 months ago by Wolfgang Huber13k
0
votes
2
answers
150
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 5 months ago by Wolfgang Huber13k
0
votes
1
answers
226
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 5 months ago by Wolfgang Huber13k
0
votes
1
answers
431
views
1
answers
Comment: C: Is there a conceptual difference between vst/rlog transforms and lfcShrink?
... ... whereas the VST is conceptually different. It looks at the trend between variance and mean in the data, and then tries to find a strictly monotonous transformation of the data so that this trend is removed. In practice, the transformation will approach the logarithm function for high values and ...
written 6 months ago by Wolfgang Huber13k
0
votes
1
answers
201
views
1
answers
Answer: A: Protein differential Expression analysis
... Julie There is no "in-principle" reason why DESeq2 shouldn't produce useful results also for count data from technologies that are not DNA-sequencing based. There are two issues: the normalization (a.k.a. size factors) the error model (Gamma-Poisson, GP) Both of these are quite generic, and w ...
written 6 months ago by Wolfgang Huber13k

Latest awards to Wolfgang Huber

Popular Question 9 weeks ago, created a question with more than 1,000 views. For DESeq2
Student 9 weeks ago, asked a question with at least 3 up-votes. For exprs function - clash with dplyr
Popular Question 12 months ago, created a question with more than 1,000 views. For DESeq2
Appreciated 12 months ago, created a post with more than 5 votes. For BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
Guru 12 months ago, received more than 100 upvotes.
Scholar 13 months ago, created an answer that has been accepted. For A: Nonspecific filtering of microarray data
Popular Question 16 months ago, created a question with more than 1,000 views. For DESeq2
Popular Question 16 months ago, created a question with more than 1,000 views. For Bioconductor-related papers -- special F1000Research collection for Bioc2016
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 16 months ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 2.2 years ago, created an answer that has been accepted. For A: How is the mean-variance plot calculated?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Processing imaging data from high throughput compound screen with EBImage
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: package specifically dedicated to a manuscript
Scholar 2.2 years ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 2.2 years ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 2.2 years ago, created an answer that has been accepted. For A: DESeq2 interacting with agricolae
Voter 2.2 years ago, voted more than 100 times.
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Deseq2 error estimating size factors -- zeros in count matrix
Scholar 2.4 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: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 2.6 years ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 167 users visited in the last hour