<div class="preformatted">Hi,
I am trying to install the paeg1acdf and probe files from the Meta
data site on to my windows platform.
paeg1 P. aeruginosa Source,Win32 Source, Win32
The paeg1acdf was installed properly but the paeg1aprobe could not be
installed. First of all the probe
directory is called "paeruginosaprobe" and can be installed with that
name. However, Bioconductor…
Order by: Relevance
expect such a function to disappear without being
deprecated, but you can always lookup the package recent changes using
the news command:
news(package="DESeq")
Depending on your R version, you can query more specific new, i.e. if...news(Version >= "1.9", package="DESeq")
As I said, since I do not expect such a drastic change in the DESeq
API, make sure as well that nothing changed in y…
do pairwise or multiple alignments(e.g. seqinr and biostrings). I, however, do not know how to probe changes at specific positions. For instance, I would like to know the best way to align a standard sequence with several mutant...and seq2 = "mutant seq", align these 2 and then have a way to ask R to report whether there is a change at position 10, or 11, or 12 and so on such that R reports(for e…
updated 10.1 years ago • debra.ragland
Ensembl marts for release 114 are now live on www.ensembl.org.
If you are using biomaRt, you can change your host to access our most recent data
Ensemblmart114 <- useEnsembl(biomart="ensembl")
PS - if you want force a previous
div class="preformatted">Hello Arne,
Several publications recently have shown that the distribution of gene
abundances seems to follow a power law (one such is referenced at
www.the...hybridization to each probe. If we could estimate this, we would be
further
along in estimating fold changes.
regards
Mark</div
I have a question regarding analysis of a common experiment in regulatory evolution using DESeq2.
The aim of the experiment is to distinguish cis and trans regulatory divergence between close species, and it is widely used on many organisms. The trick is that we profile gene expression in the two species and their F1 hybrid. We then determine allele-specific expression in the hybrid based on seq…
updated 5.7 years ago • gat.krieger
I am reanalyzing some CRISPR-Cas9 screening data to look for sgRNAs effective across cell lines.
countData:
![enter image description here][1]
colData:
![enter image description here][2]
Condition here corresponds to time (initial vs. final).
I can set up the DESeqData like this, where the fold-change result is from the effect of time:
`DESeq2::DESeqDataSetFromMatrix(countData = counts…
updated 4.8 years ago • P1000
How to change the default scatter plot colors of dba.plotMA function?
---
Senthil
updated 8.9 years ago • Senthil
M values show clustering by sex. I find it hard to figure out how going from beta to m-values can change the clustering profile. Is this normal or is something wrong somewhere? There is also this weird stripy clustering...func beta value mds.
![https://i.ibb.co/ZVRFsDQ/mds-compare-s.png][1]
Fig: MDS on beta values (left) and M values (right). Each plot shows different normalisations (raw, noo…
updated 6.8 years ago • rmf
An embedded message was scrubbed...
From: Paul Hammer <paul.hammer@p-t-p.de>
Subject: fold change calculation
Date: Tue, 19 Feb 2008 19:02:52 +0100
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updated 17.9 years ago • Paul Hammer
<div class="preformatted">Hi,
I am currently working on two channel exiqon data analysis work and I
have
questions about calcualting fold change values after normalized data.
I am using R lima package and folowing Dr. Peder Worning code(
https://stat.ethz.ch/pipermail/bioconductor/2009-March/026738.html)*
RG.MAin limma
* for getting the outputs and the code is working is excellent. But my…
updated 15.4 years ago • ashwin Vishnuvardhana
div class="preformatted">I have an Affymetrix library which I compute the fold change
and PA call for every probe with Bioconductor.
I found cases where probe may have a high fold change (>= 5)
but the Pa call...is 0.
My question is, how can we interpret such cases?
Should we assign the probe fold change to be 0 or 1?
We need to assign values because later we will
perform hierarchica…
updated 12.1 years ago • Gundala Viswanath
of columns), and I have profile data of the target (735 rows and 6 columns). I used data from [this source][1].
**My attempt**
after go through few microarray analysis tutorials on Bioconductor, I tried basic workflow as follow...which genes have a possible correlation with target data profile. How can I find out the gene that changes in expression? How can I make feature selection for load…
updated 6.6 years ago • Jurat Shahidin
Fri, Apr 19, 2002 at 08:09:59AM -0700, Dennis P. Wall wrote:
> Dear Dr. Laurent,
>
>
> I recently found your very helpful affy package and preprocessed
HU_95A
> CDF file. I am confused about how to use the cdf file...your help.
>
>
> Best,
>
>
>
> Dennis
Dear Dr. Dennis,
Thanks for your comments and for reporti…
Hi everybody,
I am not sure if I asked a totally stupid or unnecessary question here, but this is an actual question bothering me for a long time after I learned how to perform differential expression analysis using tools like limma/edgeR/DESeq recently.
We all know that the mainstream DE analysis is build on (generalized) linear model framework, and such framework is...after I learned how to p…
quite a few probe sets that are considered statistically
significant by my analysis, but have a fold change close to 1,
indicating the level of transcript is not THAT different between 2
groups. Most of the probe sets that fit
I just uninstalled and reinstalled R and all the packages I am using to see if this would help. No change.
My questions are -
- the original partial fix was to use devtools and install what I take to be modified source on github...to me, and, if not, what's up (problem was reported ~3 years ago, seems like fix should be in most recent version)?
- after the person who originally reporte…
updated 6.6 years ago • dburner1
Hi,
I would like to clarify how Ballgown computes the _fold change (FC)_?
If "group" is defined as c('KO','WT'), what value goes to numerator, and what to denominator? FC= KO/WT or FC=WT/KO
<pre
updated 9.0 years ago • Ir
Hi all,
I am trying to install RnBeads on HPC server, but keep getting below error;
source('https://rnbeads.org/data/install.R')
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing...Hi all,
I am trying to install RnBeads on HPC server, but keep getting below error;
source('https://rnbeads.org/data/install.R')
Bioconductor vers…
updated 3.8 years ago • nabiyogesh
Hi,
I've been using the shrunken log fold-changes generated by apeglm as the test statistic for gene set enrichment analyses when running the fgsea package. I have...have been shrunk & may not be appropriate for calculating S/N ratios?
Many thanks for any comments/ideas.
Cheers,
Richard
updated 6.7 years ago • coulsonr
the user
manual is that when
the sample size in each group is larger than 5, the results will keep
changing when you run the SAME code many times.
I happen to find this comes from subrountine (am.trans) called by lpe
function...y) > 5)
y <- y[, sample(1:ncol(y), 5)] # here makes
the results keep changing
n <- ncol(y)
if (n < 2) {
…
<div class="preformatted">Hi,
I would like to compare 2 RNA sources to see if a culture medium
mimetic the plant host.
There are evidence that a culture medium mimetic the plant, then I...div class="preformatted">Hi,
I would like to compare 2 RNA sources to see if a culture medium
mimetic the plant host.
There are evidence that a culture medium mimetic the plant, then
It seems next to impossible to change the size of the `geom_text()` labels with `autoplot()` in *ggbio*. For example, take the reproducible code:
require(ggbio)
require...that something like this would work:
p + geom_text(size = 16)
However, that doesn't change the size.
I also tried (before running `autoplot()`) to set defaults for `geom_text()`, but that neither works:
…
updated 6.4 years ago • Kevin Blighe
Hello,
I am not able to change seqlevels (as I think I was used to) for GRanges objects.
<pre>
seqlevels (gr) <- seqlevels (noexons1)
Fehler in getDanglingSeqlevels...noexons1)</pre>
Can anybody explain this behaviour? What is the "normal" syntax to change seqlevels?
Thanks
Hermann
<pre>
dput (gr)
new("GRanges"
, seqnames = new("Rl…
I was using an old version (v 1.16.1). It was strange because I just installed it with:
<pre>
source("https://bioconductor.org/biocLite.R")
biocLite("DECIPHER")
</pre>
Thus, I installed manually the more recent version available...pre>
install.packages("~/DECIPHER_2.0.2.tar.gz", repos = NULL, type="source")</pre>
And now it seems to be ok with the manual. Why the biocL…
updated 9.6 years ago • Vinicius Henrique da Silva
of installation can not be finished and R keep reporting errors as below:
<pre>
* installing *source* package 'org.Mm.eg.db' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package...indices
** building package indices
Error in format.default(x, width = width, justify = if (flag == "-") "left" else "right") :
8 arguments passed…
updated 10.4 years ago • affaid_tyj
the godata function in the AnnotationDbi package but I get an error. It says that two fields in the source DB have the same name. The same error raises when trying to get the keys for "GO" and "EVIDENCE".
Could you please help me to...into ‘/home/javier/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
* installing *source* package ‘org.Rleguminosarum.bv.viciae.2.3841.eg.db’ ...
…
updated 5.7 years ago • jdiaz
I am looking the log2 fold change and when I follow the steps below, these messages are appeared. What am I doing wrong?
```
dds <- DESeqDataSetFromMatrix
updated 5.5 years ago • mmortoglou97
using DESeq2 package. As these pathways are not all present in every sample, the data frame has been left with 0s in at least one spot in every row. I attempted to use my own geometric means and using type="poscounts" as well, with...mentioned in a post 3 years ago without identifying the cause of the issue with all solutions commented not working in my case(link to the thread https://support.bio…
updated 4.5 years ago • alawrence2211
I have recently found that the following query (which used to work perfectly) is now failing:
> library(biomaRt)
> ensembl = useMart...listAttributes' to get valid attribute names
Is this a bug or has the functionality of getBM() changed in a recent update? Or has the 'entrezgene' field been removed?
Thanks
updated 6.3 years ago • Miguel Juliá
function `nbinormLRT`. I was wondering what the ramifications are if I wanted to calculate fold change for example for specific timepoints.. Hypothetically could I use the `wald test` instead of `LRT` in this case to get FCs
Banking Corporation
Dear Westpac user,
The Westpac website has changed, including the sign in page.
Please login to your Westpac Online
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updated 16.2 years ago • Westpac Bank
given in previous
versions (1.5, 1.6, 1.7).
Can someone please explain to me why there has been
a change?
Regards,
Maria.
</div
updated 20.4 years ago • MARIA STALTERI
description here][3]
I even tried to start with 1000 peaks of each one that showed higher fold change but again got the same pattern for plotbox. Even the outliers are the same, How it's possible?
here is the code:
peaks_10k_three_marks_obj...TRUE,bParallel=TRUE)
peaks_10k_three_marks_obj <- dba.contrast(peaks_10k_three_marks_obj, categories=DBA_FACTOR)
peaks_10k_three_marks_ob…
updated 5.5 years ago • Mar Mar
0" cellspacing="0" style="width:475px">
<tbody>
<tr>
<td>
<p> </p>
</td>
<td>
<p>Fold Change</p>
</td>
<td>
<p>AveExper</p>
</td>
<td>
<p>t</p>
</td>
<td>
<p>p_value</p>
</td>
<td>
<p>adj.p_value</p>
</td>
<td>
<p>B<…
updated 8.6 years ago • Bioinformatics
As part of our security measures to protect your online banking
account,
Cahoot has introduced a recent internet banking security upgrade.
This compulsory upgrade requires you to authorize access to your
Cahoot
online...generated this alert will not accept replies. If you
would like
to contact us with questions or comments, visit our customer
service
section.
? Cahoot
Cahoo…
updated 16.6 years ago • Cahoot Online Banking
<div class="preformatted">Dear All.
I am starting up a new project in which we are going to do CGH on a
large set of paired samples. I have not decided on which platform I
should use to do this though. The competitors are Agilent 244k, Affy
SNP 6.0, Illumina 1M.
I have looked in the recent nature and nature genetics papers where
76 - 27 % of the CNVs detected by a fosmid approach (Mapping…
am using it to do pairwise comparisons of
RNA seq data. I just realized that the sign of the fold change will
be determined by how you label the samples in groups. So if I have T1
and T2 as my two groups, it is labeled in that order...T60 d$samples will list them in that order but the levels in
d$samples$group will sort them and that changed the sign of the fold
change. I am using the same inpu…
hello,
I am trying to change the size text of x and y axis in plotMD under EdgeR package, however I couldn't find any solution to it.
how is it possible
I am using rGREAT to annotate my Chip Seq peaks but suddenly the "availableOntologies(job)" has changed to:
[1] "GO Molecular Function" "GO Biological Process"
[3] "GO Cellular Component" "Mouse Phenotype"
[5] "Mouse Phenotype Single
updated 6.3 years ago • researcher
with
repos=NULL. See the help pages of install.packages for details, and
perhaps the source code for biocLite and biocinstall, both downloaded
when you source('http://bioconductor.org/biocLite.R').
'Automatically
datasets but still it's good to use it as a reference. It's also explained here that imprecise fold changes are shrunk and large fold changes are kept (https://support.bioconductor.org/p/77461/). And that is valid for the data...over the used methods.
Here is the data set with 3 replicates and the several methods. From the left to the right it is the following and I used coef in the lfcShrink fu…
PM
To: Lana Schaffer
Subject: Re: [BioC] makecdfenv()
>>Now I can add:
>>- go to the C source of the parser, turn the debug/verbose switch on
and
>>recompile/install the pack (then the parser will be _very_ verbose...Which gene is skipped?
>>
>>It could have something to do with the reading of lines with comment
>&g…
updated 21.5 years ago • Lana Schaffer
<div class="preformatted">Dear all,
I am evaluating a collection of two-color arrays. There are several
sets corresponding to different tissues, there is a treatment (common
for each tissue), and the treatment effect is analysed independently
in each of the tissues. I am analysing the data using limma.
The results in terms of the number of significant genes vary widely
depending whether t…
in the current release
(2.3) of Bioconductor.
If you are asking whether there have been any changes in the
annotations
for the current release (2.3) compared to earlier releases, the
annotations are always changing...sometimes more, from one release to the next.
That
is because the underlying databases that are the sources of the
annotations - EntrezGene, UniGene and RefSeq, for example - are
c…
updated 17.0 years ago • MARIA STALTERI
BioC] limma: plotMA for RGList objects
> To: bioconductor at stat.math.ethz.ch
>
> With a recent update of bioconductor it appears to me that a little
bug has
> been introduced into plotMA() in the limma package:
>...array=2) does not work
> anymore if foo is an RGList.
>
> The reason seems to be a small change in the respective part of the
s…
is exactly what the log-ratio
analysis would tell you.
On the other hand, if you average the fold changes, you get nonsense
results. The two fold changes are:
10 and 1/10
so the "average fold change is a bit over 5. So you conclude...is 10 fold down in the
unstimulated condition and the second is 10 fold up. So the two fold
change
are:
1/10 and 10
so the "average" fold change is again a bit …
Hi Rory,
Sorry for the mundane question, but I think I used to be able to change the color of heatmaps in Diffbind using col = , and now that doesnt seem to work, Now I get the following error:
> plot
updated 8.4 years ago • andrew.gehrke
I'm trying to run the example provided in the function guide, in particular I would like to change the columns annotation colors.
I've tried with column_annotation_colors parameter but the result is not good.
This
updated 5.3 years ago • simone.avesani22
samples have used a different kit for the
experiment,
and I have been asked to determine whether the change in kit is
significant.
I have done clustering and PCA and the results suggest it does make a
different, but I would like...The Institute of Cancer Research: Royal Cancer Hospital, a charitable
Company Limited by Guarantee, Registered in England under Company No.
534147 with its Registered …
updated 18.7 years ago • Daniel Brewer
preformatted">Hi Daniel,
Bioconductor 2.0 is the development version. Bioconductor 1.9 is quite
recent (Oct 9th to be precise), so I wouldn't expect any new
capabilities for it.
If you give us a bit more information as to why your...gt; needs R 2.5 (I don t understand why). There is no debian package for
R
> 2.5, so I got the R source code. R source doesn t compile because it
doesn
&a…
am doing pairwise comparisons with DESeq2 (version 1.24.0). I would like to shrinkage the log2 Fold Change using the normal approach. I used the following code:
dds <- DESeqDataSet(se_sel, ~ condition)
dds <- DESeq(dds)
resNorm...dds, contrast=c("condition", cond1 , cond2 ), type="normal")
resNorm
log2 fold change (MLE): condition cond1 vs cond2
…
updated 5.7 years ago • dequattro.concetta
on [www.ensembl.org](http://www.ensembl.org/index.html).
If you are using biomaRt, you can change your host to access our most recent data:
ensembl\_mart\_84 <- useEnsembl(biomart=“ensembl")
* Ensembl Genes 84...to "Activity" in the "Regulatory feature" dataset
* Vega 64
A complete list of the changes in release 84 can be found at&nb…
new Ensembl marts for release 90 are now live on www.ensembl.org.
If you are using biomaRt, you can change your host to access our most recent data:
<pre>
ensembl_mart_90 <- useEnsembl(biomart=“ensembl")</pre>
Ensembl Genes 90
* Addition...Variation 90
* Updated human variation data
You can find the complete list of the changes at <http://www.…
Hi everyone,
I am trying to plot Volcano plots for analysis mostly from Limma. I found 2 sources- one that labels points above certain thresholds of adjusted p values and logFC values and another one that uses...Hi everyone,
I am trying to plot Volcano plots for analysis mostly from Limma. I found 2 sources- one that labels points above certain thresholds of adjusted p values and logFC values a…
updated 8.2 years ago • Nithisha
findOverlaps documentation mentions that G/IRanges is moving a Nested Containment List objects implementation with slightly changed behaviour. The documentation mentions that special meaning of maxgap in conjunction with start/end...that G/IRanges is moving a Nested Containment List objects implementation with slightly changed behaviour. The d…
updated 10.6 years ago • Daniel Cameron
Hi,
We are trying to understand DEseq2 fold change values.
Here I am giving example of some genes with their normalized read count values and calculated log fold change...Hi,
We are trying to understand DEseq2 fold change values.
Here I am giving example of some genes with their normalized read count values and calculated log fold change.
__Normalized Read count values__
<table border="0…
updated 8.4 years ago • madhusudhana.janga
I would think that the dots with a rectangle (1,2,3) can be considered as outliers and might be left out for further differential expression analysis (between treatments).
However, this is just based on visual inspection...considered as an outlier (instead of just by visual inspection of PCA, like most papers do).
In a recent paper of Conesa et al 2016 ([https://genomebiology.biomedce…
updated 9.1 years ago • wd
fractionation.
The idea of collecting input is not only so that we can look at
transcriptional changes but to normalize to something that would be
free of
the technical variation and RNA loss that polysome fractionation...by input counts
per
gene/feature => edgeR differences between genotypes across
polysome/rnp/input categories
My question is thus: Is there a way to tell edgeR to normal…
Dear Bioconductor support team,
I have samples from two time points namely __V1 and V4__. The samples belong to two categories: Treatment and Placebo as follows:
005v1 Placebo
005v4 Placebo
008v1 Treatment
008v4 Treatment
The ID number 005 etc represent the __same sample at two time__ points. At V1 time-point there is no treatment given, its just that the __samples are a…
updated 7.0 years ago • candida.vaz
Recent ...
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Hope you don't mind I am not Johannes... ;-)
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