as well as the odd numbered development versions 2.9
and 2.11). There is no added functionality nor bug fixes so current
users of Rgraphviz do not need to update their version.
Some added comments on (R)Graphviz:
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<div class="preformatted">Dear BioC,
I’m running a metabolomics experiment using samples that were
collected from years 1999 to 2006. The study is unbalanced as the
diseased
samples were taken in all years, the controls only in year 2000 and
2001.
The sample size per year varies from 8 to 29 per year.
For some metabolites the measured intensities are significantly
different
between sample…
updated 19.2 years ago • E. Schwarz
based on a channel and an transformList generated by estimateLogicle, but neither the approach, nor my implementation are elegant by any stretch of the imagination. If there is a more suitable way that I might have missed
6448 3550
http://www.genopolis.it
Press ENTER to look up in Wiktionary or CTRL+ENTER to look
up in Wikipedia
</mirna-1_0.ann></serial></mirna-1_0.prb></mirna-1_0></cfa-mir-219-star_st></mdv1-mir-m9-star_st></hsa-mir-664-star_st></hsa-mir
updated 15.6 years ago • giacomo.tuana@unimib.it
or the
standard
> deviation (as documented on the man page)? Also is it before or
after the
> log(2) transformation (I guess it is before, but want to make sure)?
>
> Thanks again for taking your time to answer my questions...packages/devel/bioc/html/vsn.html
> and unpack it. See the file vsn2.c. There is also public, anonymous
svn
> access, which is des…
be normalised or transformed in any way prior to loading into the TMixClust function, for example log values or log fold change values of FPKM/TPM.
Can one use scaled/log transformed/fold change data with TMixClust?
Thanks
updated 6.1 years ago • astridite
ExperimentHub, but some resource will be used in this package, such as GATK Panel-of-normal data, is public. So I am not sure whether it is suitable for us to build an annotation package using public dataset.
Do you have any suggestions
updated 23 months ago • Xin Wang
from database. This may take several minutes until next notification.
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line
updated 10.1 years ago • albert.ayoub
adjusted to avoid
# changing the magnitude of the counts.
normMat <- normMat/exp(rowMeans(log(normMat)))
normCts <- cts/normMat
# RSEM produce 0 effective length
# Computing effective library sizes from scaled counts...Combining effective library sizes with the length factors, and calculating
# offsets for a log-link GLM.
normMat <- sweep(normMat, 2, eff.lib, "*")
…
1 vs Group B Condition 2 I could think of would be to normalize the counts for each, compute the log fold change, and see if there are any genes with greater log fold change than some predefined threshold or upper quartile...of the significant genes log fold change that are not already significant. Another would be to create a fake Condition that is set up so that instead...although all of the pv…
updated 5.8 years ago • august
is no such thing. In
statistics there are assumptions you make about the underlying data,
and if you violate the assumptions then your results may not mean what
you think. I wouldn't say it is 'incorrect' to violate assumptions
updated 18.6 years ago • James W. MacDonald
and to the 'devel' repository for nightly cross-platform builds and distribution to the general public. The review process means that the package is previewed by a single person, often with limited expertise in the scientific...process will be established over the coming months. Broadly, new package submissions will be to a public rather than private issue tracker. Packages will continue to be su…
updated 10.0 years ago • Martin Morgan
output have been adjusted for purity. Does this also hold true for the "mean" values for mean log ratios? It appears to me that they are adjusted for purity (but are still log mean ratios, not actual mean ratios and not
updated 7.6 years ago • twtoal
Hello,
I do not manage to really understand if the DESeq2 normalisation and regularized log transformation are taking the size of the gene into account. Do they?
It seems to me that they are not...But I am probably missing...find differentially expressed genes or when I am looking at expression profiles after a regularized log transformation ?
Many thanks
updated 10.7 years ago • AurelieMLB
in identify genes with genotype:condition interactions. The res objet report p-values but also log fold change. How can I make sense of these fold changes? At least how can interpretive negative from positives log fc
updated 9.8 years ago • colaneri
on this function to calculate fold changes.
1. is there a better way to calculate.
2. how do i get log-fold changes.
fc <- function(x,CL0,CL1){
x0 <- x[,CL0]
x1 <- x[,CL1]
res <- (apply(x0,1,mean) - apply(x1,1,mean))
}
foldcs
<-fc(mydata_mat,CL0...farm.cl==0),CL1=(fram.cl==1))
logfoldcs <- log(foldcs,2) OR loggoldcs <-
l…
fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc@channing.harvard.edu
-----BEGIN PGP PUBLIC KEY BLOCK-----
Version: PGP 6.5.8
mQCNAzqIeGUAAAEEAMJXU941vIornTS52rl6z7eo+A7wwB0km/idLnkxzIhc1uLi
Qtn19OyOfG6IDSucLrtmpvwagemAnQ9jL6TVDrmlrKnqsh...DhhtT4mEAHt0E8dNBVCj+lKr3W
vYS5GqO9gY4CiT3JXFH9N19pSbUQFiNDqpmG6EbWng==
=DQNF
-----END PGP PUBLIC KEY BLOCK-----
</div
updated 23.8 years ago • Vincent J. Carey, Jr.
to be set:
R_DEFAULT_PACKAGES: NULL
This variable is not set when I start an R session, nor is set after simply loading the library package. It only exists after calling "run_mofa". It persists in the separate R sessions
to geometric mean per gene), shall I just use the following codes without using (normTransform) nor (vst) functions?
# dds <- estimateSizeFactors(dds)
# mat <- counts(dds, normalized=TRUE)
2. My understanding is that the function
updated 2.8 years ago • phmai1148
line 1, column 11797, byte 11797 at
/usr/lib/perl5/XML/Parser.pm line 187
does not seem to be XML, nor to identify a file name
> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-pc-linux-gnu
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC
429 back:
```
< HTTP/1.1 429 Too Many Requests
< Server: CloudFront
< Date: Thu, 10 Mar 2022 16:29:06 GMT
< Content-Length: 0
< Connection: keep-alive
< X-Cache: Error from cloudfront
< Via: 1.1 040f8a2cdffe1cf7a35d28e06c3ed574.cloudfront.net
updated 3.8 years ago • tshouler
Hi!
I am not sure I understand well the parameters alpha and lfc Treshold of this function : results {DESeq2}
I first understood that these parameters allows to choose a p value and log fold change threshold, for example if I chose a pvalue of 0.05 and a log fold change of two then I exptected to only keep the genes with a p-values >0.05 and an absolute log fold change >2..&nb…
and I get this error:
<pre>
> library(biomaRt)
> listMarts()
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line...body line 4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYS…
should be placed in three backticks as shown below
```r
cpm <- cpm(dge)
lcpm <- cpm(dge, log=TRUE)
L <- mean(dge$samples$lib.size) * 1e-6
M <- median(dge$samples$lib.size) * 1e-6
c(L, M)
lcpm.cutoff <- log2(10/M + 2/L)
library(RColorBrewer...1]), col=col[1], lwd=2, ylim=c(0,0.55), las=2, main="", xlab="")
title(main="A. Raw data", xlab="Log-cpm")
abl…
updated 24 months ago • Shaimaa Gamal
if the arrays are paired with one
treatment
and one control in each rep you can do the following:
M= log(trt)-log(ctrl)
A=(log(trt)+log(ctrl))/2
loess.out=loess(M~A)
norm.data=loess.out$residual
You will get one normalized value for
Hi all,
After reading about voom, limma and GLM, I highly get confused about link functions and voom. The log transformation of counts in limma-voom, is the logarithm serve as a link function in the GLM formalism or is it merely a scale...After reading about voom, limma and GLM, I highly get confused about link functions and voom. The log transformation of counts in limma-voom, is th…
Has anyone tried demo(affy.tour)i n BioC2.6? I
am
getting the error message:
image(cel,transfo=log)
Error in image.default(cel, transfo = log) : argument must be matrix-
like
In addition: Warning message:
In data(cdf.example
Hi,
I am trying to build an annotation library using SQLForge for a custom microarray that targets endogenous retroviruses in the human genome (HERV). The goal is to access and if possible visualize public annotations (polymorphisms, conservation across species, epigenetic modifications, etc.) associated with a list of...endogenous retroviruses in the human genome (HERV). The goal is to access a…
updated 11.0 years ago • becker.jeremie
list,
I'm trying to use the package GenomeGraphs to visualise custom genome
data (genome not in public databases). In the corresponding
publication to genomegraphs (Durinck et al. BMC Bioinformatics, 2009 )
I found the partial
updated 16.4 years ago • Michael Dondrup
__Full details and application link at __[__http://www.jobs.cam.ac.uk/job/16356/__](http://www.jobs.cam.ac.uk/job/16356/)
__Application Deadline: Sunday 11th February 2018__
__Background:__
The MRC Cancer Unit (MRC CU) is a University Department situated on the Cambridge Biomedical Campus. It provides an outstanding environment for cancer research, supporting some 10 research groups and ~100 b…
updated 7.9 years ago • Shamith.Samarajiwa
<div class="preformatted">Hi,
We upgraded from BioC 2.0 to BioC 2.4. Now I note that log-intensities
computed by gcrma differ from the values I got previously, for the
same
input.
For example, for one array the mean ratio of old vs new log-
intensities
is 0.9996 with an sd of 0.0187.
For a second array, analyzed in the same set, the mean and sd values
are
0.9991 and...div class="preformatte…
KO1, KO2). I want
to find genes that are significantly changed with the following
property:
sign(log(ON/WT)) == -sign(log(KO1/WT)) and -sign(log(KO2/WT))
would the following design and contrast matrix be correct
type = is a factor with levels
v 1.14.2) function calculateTangentNormal the tumor fragment counts are denoised creating a sort of "log-ratio" which is then converted to average coverage and this average coverage is used later on to calculate the log-ratio...be used in the segmentation. Was curious why segmentation isn't done on the denoised fragment counts/log-ratio. Does this have something to do with how the fragment counti…
updated 6.1 years ago • sruddy17
gt;>
>>> I just had another quick question. The targets are
>>> ranked by the log-likelihood. Does this mean that the higher the
>>> log-likelihood the greater the probability of the gene being a
target...gt;>>or
>>> vice versa? Also what does null log likelihood stand for?
>>
&a…
Dear Communities,
As the author of limma suggested, the Log-transformed RSEM expected count could be reversal of the log-transformation and then feed to voom without round (https
updated 3.5 years ago • Yang Shi
<div class="preformatted">There are a couple of things you can do. Using the siggenes package
you
can take your log ratios and calculate one-sample t-statistics, where
you are testing to see if the mean of the ratios differs from zero.
This
is probably the easiest thing to do.
If you want to convert your data back to log intensity values, you can
then either use siggenes or multtest. In th…
updated 22.2 years ago • James W. MacDonald
CRAN: https://cran.rstudio.com/
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31)
Installing package(s) 'annotables'
Warning message:
package ‘annotables’ is not available for Bioconductor version
updated 2.9 years ago • m-bihie
bioconductor at r-project.org
> Subject: [BioC] Limma - RNA-Seq DE genes - Quantile normalized log
> transformed RPKM data
>
> Hello All,
>
> I'm trying to understand the method of differential expression
analysis
e.g. norm-exp in limma. We did not have this type of distribution in version 3 of HT12, nor in any other chip type from Illumina. Has anyone else seen this particular issue, and specifically on the HT-12 v4 chip?
Below
not find any reference to that HUMANREF-8_V2_11223162_B
annotation (neither on Illumina website nor in Bioconductor packages).
I
only found information about HUMANREF-8_V2_11223162_A. Is the letter
suffix (A or B) really
updated 17.1 years ago • Renaud Gaujoux
When I try to save a SWeave file, I get a message that I need to
install TeX first. But neither Tex nor LaTeX seems to be available for
R 3.0.3.
> biocLite("TeX")
BioC_mirror: http://bioconductor.org
Using Bioconductor version
updated 11.8 years ago • Guest User
people,
I am trying to reproduce a microarray analysis from the publicly
available raw data of a publication.
The pre-processing method is detailed in the Methods (robust multi-
array
analysis with quantile normalization...come from the version of my affy package
(current bioconductor package version): the authors in the publication
used affy package v1.5.8. However, the 1.5.8 is not available …
updated 16.9 years ago • Leonor Palmeira
Hi Mike and others,
I want to use apeglm for effect-size shrinkage in a (normal) linear regression setting and I'm interested in shrinkage of almost all of the model coefficients. Here's a toy example:
library("apeglm")
library("DEP")
library("limma")
library("SummarizedExperiment")
library("dplyr")
# load data
data <- UbiLength %>%
filter(R…
Biostrings * 2.58.0 2020-10-27 [1] Bioconductor
bit 4.0.5 2022-11-15 [1] CRAN (R 4.0.2)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.0.2)
bitops 1.0-8 2024-07-29 [1] CRAN (R 4.0.2)
blob 1.2.4 2023-03-17 [1] CRAN (R...futile.options 1.0.1 2018-04-20 [1] CRAN (R 4.0.2)
generics …
<div class="preformatted">Hello,
I have some 2-color microarrays that I need to analyze as single
channel because some of the conditions I want to compare are
unconnected. I've been trying to follow the example in the
limmaUsersGuide() on "Separate Channel Analysis of Two-Color Data".
However, it appears that neither
normalizeBetweenArrays(method="Aquantile") nor the lmscFit() function
use…
updated 15.8 years ago • Jenny Drnevich
this error
<pre>
library(minet)
Ed=discretize(t(E), disc="globalequalwidth",nbins=ceiling(1+log(ncol(E))))
<span style="line-height:1.6">Error en discretize(t(E), disc = "globalequalwidth", nbins = ceiling(1 + : </span>
unused arguments...disc = "globalequalwidth", nbins = ceiling(1 + log(ncol(E))))</pre>
<span style="line-height:1.6">thank you</span>…
updated 11.2 years ago • sleidymagaly
low purity (about 0.2). PureCN has flagged most samples as having very low purity and noisy log ratio. I presume that the low purity causes the noisy log ratio? We are planning to sequence additional DNA from
updated 7.6 years ago • twtoal
in
thousands
of books and articles on glms. It corresponds to your first formula
for a
glm with a log-link.
One should be very careful about using established technical terms in
a
way that conflicts with the established...of the
hand-off to provide an explicit formula for what is meant by "offset",
which could be one of:
log(mu) = X * beta + offset
log2(mu) = X * beta + offset
log(mu) + offset…
exon length when testing for DE. In the voom paper it
is
mentioned that although voom is based on log-cpm values, it "/can work
however just as easily with logged RPKM values in place of log-cpm,
because the precision weights...are the same for both measures. If the
genomic length of each gene is known, then the log-cpm values output
by
voom can be converted to log-RPKM by subtracting the log-bas…
Hi all,-
I want to compare logFC value from the output of exactTest function in
edgeR
for two different comparisons for each gene. So I have 4 conditions
and I
am testing if logFC for conditions 1 and 2 in that order is the same
as
logFC for conditions 3 and 4 in that order. What will be the right
statistical test and is there a function in R to do this?
Thanks
Al
[[alternative HTML ve…
updated 12.5 years ago • Alpesh Querer
Dear Bioconductors,
I would like to generate a scatter plot of single colour array data
where;
1) up-regulated genes with FDR <= 0.05, points are coloured in red
2) down-regulated genes with FDR <= 0.05, points are coloured in blue
3) all other points are in green/other colour
I know I can do volcano straight from Limma but a simple scatter plot
with
colours would be useful.
Thanks.
…
Dear Bioconductors,
I would like to generate a scatter plot of single colour array data
where;
1) up-regulated genes with FDR <= 0.05, points are coloured in red
2) down-regulated genes with FDR <= 0.05, points are coloured in blue
3) all other points are in green/other colour
I know I can do volcano straight from Limma but a simple scatter plot
with
colours would be useful.
Thanks.
…
Hi,
I need to calculate some data regarding the variance of probes across
samples. Typically we have expressed this as the relative standard
deviation before. However, I have only done this for 1 colour data
previously and the dataset I am working with is 2 colour common
reference data. When I repeat what I did previously using the Ratio I
see very strange (High) percentages. When I use only tar…
updated 14.5 years ago • elliot harrison
of logarithmic channels depend on the $PnE parameter, which contains f1 and f2. F1 specifies the log range and f2 the minimal value on the linearized scale matching the zero value on the log scale. (This can be referenced in...implemented as 10^((x\*f1/range)\*f2). This would - in my understanding - wrongly scale the obtained log scale values. Eg an f2 minimum of 0.1 could only map to 1 on the sc…
updated 7.9 years ago • max.zhao
expression data.
The help page says:
Note: If your 'BSData' object contains data already on the
log-scale, be careful that you choose an appropriate 'transform'
to avoid logging it twice. The same applies for the '"vst"'
transformation...in 'BSData' to be on the original
(un-logged) scale.
Does with mean that a transformation to log scale (via log or glog)
happens _o…
updated 17.9 years ago • Simon Anders
think that they are already normalized.
When I open txt file in R studio, I can have RPKM, P value, log fold change and base mean and other specifications.
I am wondering which one I need for generating heat map. I assume that...remove all the columns but logfold change columns and then start analysis. I am not sure if I need log fold change or log2 fold change though
updated 5.9 years ago • alirezabcsaeidi
then it is fitted to linear model and eBayes function is used to
summarize
the statistics.
Finally log odds is used to rank the differential genes.
I am wondering is the log odds rank the genes which express different
between
updated 19.5 years ago • yanju@liacs.nl
documentation, "all matches must additionally satisfy
the minoverlap constraint". This constraint is violated when a zero-
width range is passed as the query parameter with a non-zero maxgap. I
presume this is a bug, is it not?
rangeZero
updated 12.3 years ago • Guest User
<div class="preformatted">Dear Stephen,
As I understand it, from a Rosetta seminar I attended nearly a decade
ago,
Rosetta Resolver fits a statistical model to all the genes
simultaneously
that allows it to assign p-values for a single array, i.e., without
replicates. I don't know whether the Rosetta method has been
published,
or whether it's purely proprietry, but however it works it see…
updated 14.0 years ago • Gordon Smyth
Recent ...
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Comment: Guitar R package requires update due to dependency GenomicFeatures
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I followed your recommendations and generated a [pull request][1] including the fix for this issue…
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Guido Hooiveld
★
4.1k
Hope you don't mind I am not Johannes... ;-)
Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
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jtsy6383
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0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
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jwp48
•
0
Dear Johannes,
Would it be possible to generate a EnsDb for the newest Medicago V5 genome release?
Medicago truncatula A17 r5.0
This woul…
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
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Ludwig Geistlinger
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When referring to the OSCA book including individual sub-books please cite the OSCA paper:
Amezquita, R.A., Lun, A.T.L., Becht, E. et a…
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