div class="preformatted">Edmund,
On Thu, 24 Jun 2004, Edmund Chang wrote:
> I am going through the tutorial now and I encountered a problem with
> the top table
> 'Error in unlist(multiget...know how to
> correct this problem.
Sorry, affylmGUI was using the "multiget" function which is
recently been replaced by "mget". It is fixed in version 1.1.3,
available from…
Order by: Relevance
style="height:300px; width:300px"/>
Does this look right? It almost looks like the fold changes have not been shrunken! Is that the case?
Am I doing something wrong?
Thank you
updated 11.2 years ago • enricoferrero
<div class="preformatted">Hi Weiwei,
By default pathview sum up the gene (or compound etc) data mapped to
one node, which works well in common conditions. But you may specify
other methods, like taking mean, median, max etc of these mapped gene
data. Check the help information within R with the following lines:
library(pathview)
?pathview
Look under argument ?node.sum?.
And look on argument…
preformatted">Dear all,
The new Ensembl marts for release 72 are live on www.ensembl.org.
You can change your host to access our most recent data:
mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",
host="www.ensembl.org", path...sections.
Reinstated structural variation strains for Mouse
A complete list of the changes in release 72 can be found at
http://www.ensembl.org/info/webs…
Hello everyone,
I have a doubt about the cutoffs in DESeq2 related to padj and fold change. I initially did all my analyses using the default parameters in "results" function. Afterwards, I decided to use cutoffs
updated 9.3 years ago • pmpierry
I also collected mRNA for both wildtype and knockout. I'm interested in comparing translation changes between knockout and wildtype (and most interested in the change in high polysome relative to changes in mRNA). ...and only pulled out the ratio that I was interested in. However, I noticed that the samples I put in changes the number of significant genes a lot even when I only pull out t…
The vignette states that:
> Instead, one need only run `nbinomWaldTest` to re-estimate MLE
> coefficients – these are necessary for `apeglm` – and then run `lfcShrink`
> specifying the coefficient of interest in `resultsNames(dds)`.
>
> We give some examples below of producing equivalent designs for use
> with `coef`. We show how the coefficients…
Hi,
I would like to know, how to change the column width of the HTML table in ReportingTools. I tried to use the hwriter function, but this results in a complete...Hi,
I would like to know, how to change the column width of the HTML table in ReportingTools. I tried to use the hwriter function, but this results in a complete layout change of the table:
rpt.df <- rpt.df\[sub,\]
imagena…
updated 10.3 years ago • benedikt.athmer
RG)
design=c(1,-1,1,-1,1,-1)
fit <- lmFit(MA, design)
.
what direct are the fold changes I get out in
does a positive FC mean up regulated in the 27day sample?
Thanks
(ps I would've found it useful if 'coefficients
updated 17.5 years ago • Glyn Bradley
I have one simple goal:
```
gr <- GRanges(seqnames = c("chr1", "chr2"),
ranges = IRanges(start = 1:2, end = 4:5))
```
I want to change the chromosome names all to "chrX"
```
> seqnames(gr) <- "chrX"
Error in .normalize_seqnames_replacement_value(value, x) :
levels...c("chr1", "chr2"),
ranges = IRanges(start = 1:2, end = 4:5))
```
I w…
updated 4.2 years ago • changxu.fan
This is BiocCheck version 1.15.9. BiocCheck is a work in progress. Output and severity of issues may
change. Installing package...
\* Checking if other packages can import this one...
\* Checking to see if we understand object initialization...Checking for non-trivial biocViews...
\* Checking that biocViews come from the same category...
\* Checking biocViews validity...
\* Chec…
updated 7.7 years ago • topijush
Hi,
I have a quick question regarding plots. I have previously created a plot such as this to look at the log2fold change between treatments, but I now have an interaction effect between treatment and different time points. I attempted to recreate the same plot, 9 times, as to compare treatment _T1 and Treatment_T2 etc and see how the plot changed but the plot is always the same. Therefore I…
I have found some cases where the fold change values don't make sense to me, and I am wondering if I hit some edge case bug. Here is one example, notice that row 3 has...more MUT1 counts than rows 1 and 2, but a lower fold change.
<pre>
WT_1 MUT_1 log2FoldChange
1 0 3 2.348419e+00
2 0 3 2.348419e+00
3 0 16 2.225513e+00
4 2 3 …
updated 9.9 years ago • jgranek
in clusterProfiler R package. When specifying showCategory, I get the right number of categories except with the results of compareCluser().
In my case, I use compareCluster() on a list of 3 elements:
<pre>
str(ClusterList...dotplot(CompareGO_BP, showCategory=10, title="GO - Biological Process")</pre>
I ask for 10 categories, but I get 15 categories in All,…
updated 9.2 years ago • Jane Merlevede
My collaborator is requesting the following -
> A single DEG containing fold change STIM vs. UNS in MDD vs. fold
> change STIM vs. UNS in HC
I would like to know, it this possible with DESeq2? I am currently using
updated 3.6 years ago • athira
by GEO to provide a file that has not been preprocessed
fully.
However, perhaps because of minor changes, the resulting number of
probes
excluded changes from what I had documented in the past (using the
same
script).
It seems
<div class="preformatted"><reposting "r-help="" at="" from="" r-project.org"="">
Esteemed BioC user's,
I'm struggling to achieve some details of a heatmap using heatmap.2():
1. Change label locations, for both rows & columns from the default
right & bottom, to left and top.
Can this be done within heatmap.2...Esteemed BioC user's,
I'm struggling to achieve some det…
updated 15.5 years ago • k. brand
div class="preformatted">Hi James,
Thanks for your email. I'm sorry if the order of my recent email was a
bit deceptive. The version I gave was what I was running before I
upgraded. Thanks to Gordon's comments yesterday
<div class="preformatted">Dear Alex,
Do you have the same number of replicate spots for every gene of
interest
and are the replicate probes identical? If so, see the case study in
limma
User's Guide on "Within array replicate spots".
If only some of your genes are replicated, or if the probes are not
identical, I would strongly advice you not to attempt to pre-emptively
average the spots.…
updated 20.2 years ago • Gordon Smyth
new Ensembl marts for release 99 are now live on www.ensembl.org.
If you are using biomaRt, you can change your host to access our most recent data:
ensemblmart99 <- useEnsembl(biomart=“ensembl")
Important: Please note that
http://postimg.org/image/bxh4n8b1d/)](http://postimg.org/image/bxh4n8b1d/)
Hi, How can I change the font size of the y axis title? So I want the "coverage" title with bigger font. Please see the image above.
plotTracks
updated 9.6 years ago • yuyaxuan0
Hi!
I use the function dba.report to retrieve differentially bound sites (th = 1)
I found the fold-changes tend to be very small and do not know how to compute them.
For example, at one site
the mean for control is 1.6973 while...Hi!
I use the function dba.report to retrieve differentially bound sites (th = 1)
I found the fold-changes tend to be very small and do not know how to compute them.…
First of all I've searched bioconductor support and other sites without success, if I just didn't find the answer I would love if someone could give me a link.
I'm trying to get into bioconductor, I do statistical work in R and I would love to fully migrate to this platform but I've hit a rock, probably because I'm really new to genetic-related-statistics.
I've performed…
updated 9.9 years ago • fandresp
be used input. In the MAST paper, page 10, it mentions the input data are "log2(TPM + 1)." In this comment (https://github.com/RGLab/MAST/issues/147#issuecomment-770277174), Finak says "The input data SHOULD be log2 transformed...If you do not log2(x+1) transform the data you will have meaningless estimates of log fold change since the data are assumed to be on the log scale." There are multiple …
updated 15 months ago • james.watson1
<div class="preformatted">Dear all,
A draft of the BioConductor posting can be found at the following URL
:
http://neelix.molbiol.ox.ac.uk:8080/cgi-bin/ramasamy/wiki.cgi?
BioConductor_Posting_Guide or alternatively http://tinyurl.com/3kswc .
For those who are familiar with the wiki system, please feel free to
make changes. I only ask that you set your username (by clicking on
the
"Prefer…
updated 20.7 years ago • Adaikalavan Ramasamy
Do I need to specify coefficient in the glmLRT() function? I am not sure what coefficient mean, if I change it from 2 to 3 or 2:4?
lrt <- glmLRT(fit, coef = 2)
I appriciate any comments
updated 6.5 years ago • Victoria
a look in the NEWS section of the DEXSeq package, but i couldn't
find
any information about major changes.
thank you very much, regards,
[[alternative HTML version deleted]]
</div
<div class="preformatted">Dear Memebers,
I want to be able to reference individual arrays in an abatch like so
abatch[,1], abatch[,2] etc.
This seems to work fine using the original pData for the abatch after
using ReadAffy():
sample
N10S.CEL 1
N11S.CEL 2
N12S.CEL 3
N7S.CEL 4
N8S.CEL 5
N9S.CEL 6
P1S.CEL 7
P2S.CEL 8
P3S.CEL …
updated 17.7 years ago • Paul Geeleher
div class="preformatted">Dear Chao-Jen,
I recently noticed that the iFlow package was back up on the devel
branch of Bioconductor, but I got an error message when I tried...it:
> source("http://www.bioconductor.org/biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
> biocLite("iFlow")
Using R version 2.12.1, biocinstall version 2.7.4.
Insta…
hardcoded attrubutes
that it
tries to retrieve from the Ensembl BioMart database. As you noticed
recently the "biotype" attribute has changed in the Ensembl BioMart
and
we're currently enable to retrieve that from the Ensembl...an internal error, please report.
>
> I think that is a problem with biomaRt. Something have changed on
the
> biomaRt server ?
>
> Tha…
updated 17.0 years ago • steffen@stat.Berkeley.EDU
plotDensities.default()` to see the distribution of my read across sample.
Would it be possible to change the font size and axis labeling in the graph?
I used the argument `xlab` and `ylab` options, but did not see the name I wanted
div class="preformatted">Dear list,
I updated R from 2.6.2 to 2.7.2 recently but keep getting the error
"figure
margins too large" when plot pictures which never happened to me when
using
2.6.2...legend disappears in R 2.7.2. After asking R mailing
list,
they think it's something specifically changed in image() of affy
package,
especially add.legend argument. But I dont know how to fix it or
…
updated 17.3 years ago • Hui-Yi Chu
file into the package. This was the file format that was
first
used in readBeadLevelData, but we recently changed it to accept tif
images
instead (ie the images that come straight off the scanner). Try
reading the
tifs and...see if that works.
Hope this helps,
Mark
PS we are currently making some changes to the package which will make
the
reading of bead level data easier and more efficient. T…
you want to
answer and what analysis you're going to do.
If you have lots of time points so that changes between consecutive
time
points will be small, then more time points might be better than
replication. If you're just...to assess differential expression, and your time points are
such
that genes may substantially change their expression levels between
consecutive times, then I cannot see any…
updated 22.4 years ago • Gordon Smyth
I am curious about why the calculated log2 fold change value differs from the log2FoldChange of DESeq2 and want to know the cause.
Result (three condition/ Total 16 samples...Condition 1 average: 5.496522
Condition 2 average: 6.401083
Calculated log2 fold change: log2(6.401083/5.496522) = 0.219797
log2 fold change (MLE): condition Condition 2 vs Condition 1 : -0.00487575611632497.…
updated 6.5 years ago • cycy
to make sure whether the model is make sense?
2. Does the logFC got from topTable mean the fold change of gene expression for each year of age?
Kind regards,
Kasit
 
updated 7.5 years ago • KCLiv
Greetings,
I have used edgeR to calculate fold-changes in gene expression between treated and untreated cells, each group consisting of three replicates. The boss would...very much like me to display some estimate of error in fold-change for genes of our immediate interest. Is there a way to do this in edgeR? I have not found any leads in newer vignettes.
Thanks
pathway/hsa04933). Our study is not about diabetic complications but about inflammatory changes (which also activate AGE-RAGE signaling) and that is why I ask myself if it is accepted to shorten the pathway name to
on comparing tumor and healthy samples with DESeq2. My analysis only cares about the adjusted Fold Change values that DESeq2 computes.
The input data encompasses a huge number of samples (I'm working with TCGA and GTEX data...Is there a way to speed the process up given the fact that I merely require the adjusted fold change instead of the whole DESeq2 output?
The full script that I run on th…
updated 2.2 years ago • Luca
are not well correlated with the read counts data that I have.
e.g.:
for gene Glyma12g14980.1
fold change (lg Fc) = 33.21571049
Read Count: Control 1= 20, Control2= 136, COntrol 3= 15, P1= 0, P2=
0, P3= 0
Glyma10g03970.1
Fold Change= -37.80306427
I am analysing single cell seq data from Maynard et al. and I am getting strange log2 fold change values for a cluster of genes when calculated with DESeq2. When I manually calculate the log fold change this doesnt...I cant understand what is causing this. Using code on another help forum I have plotted the log fold change values so you can see the cluster I am talking about (there are also a cou…
updated 2.8 years ago • Layla
I am attaching the picture of the filtered results, I am still getting log2fold change values in negative [output of the filtered results][1], how should I resolve this?
[1]: /media/images/3548f740-8f23-4df3-bc1b
updated 22 months ago • Aaliya
each feature. This is not the case where you have just 20 or so different features (OTUs, genes, etc.). Changes in the true proportion of any of these features 'causes' changes in the proportion of the others, even if there is no biologically...meaningful change."
This comment leaves us in a methodological limbo. Shall we go for massive expansion of our mock community in order to
div class="preformatted">Hi there,
I am wondering if you can change the ECs for each enzyme on the kegg
graph
like pyrimidine metabolism into gene symbol, for example?
thanks,
Weiwei
[[alternative
updated 12.4 years ago • Ed
<div class="preformatted">I am using edgeR to analyze RNA-Seq data. This is my script:
library("edgeR")
#############################
#read in metadata & DGE
#############################
composite_samples <- read.csv(file="samples.csv",header=TRUE,sep=",")
counts <- readDGE(composite_samples$CountFiles)$counts
#############################
#Filter & Library S…
We recently got a paper rejected for publication. Initially, two reviewers accepted the paper, and one reviewer rejected it...We recently got a paper rejected for publication. Initially, two reviewers accepted the paper, and one reviewer rejected it, under the argument that having only two replicates per condition (control plants and plants infected with a fungus) does not produce reliable result…
updated 5.2 years ago • jovel_juan
<div class="preformatted">Alastair Droop <apd500 at="" york.ac.uk=""> writes:
> I found the bioconductor message annoying enough to track down and
remove.
>
> The message is displayed from within the .onAttach function within
the
> Biobase package.
It uses the message function so that you can do:
suppressMessages(library("Biobase"))
Or for many packages…
<div class="preformatted">Hi DEXSeq users/developers,
I have used DEXSeq successfuly for genes with many exons and really
like the diagnostic/visualization plots that come with it. Recently
though, for genes with two testable exons, I am getting the
"Underdetermined model; cannot estimate dispersions." error...for genes with many exons and really
like the diagnostic/visualization plots th…
preformatted">Dear all,
The new Ensembl marts for release 73 are live on www.ensembl.org.
You can change your host to access our most recent data:
mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",
host="www.ensembl.org", path...citation section
Removed "phenotype name" from the attribute section
A complete list of the changes in release 73 can be found at
http://www.ensembl.org/…
updated 12.3 years ago • Thomas Maurel
Hi
I've recently done some DE analysis with DESeq2, with relatively small sample sizes. The experimental setup is a time course of...Hi
I've recently done some DE analysis with DESeq2, with relatively small sample sizes. The experimental setup is a time course of 4 points, with matched samples of two different tissue types from 7 patients (so 56 samples in total). I've tested t3 against t0 in b…
updated 9.9 years ago • willmacnair
project relocated from Seattle, Washington
to Buffalo, New York and along with the geographical change came a few
staff changes.
A big thank you to Marc, Sonali and Paul for their contributions to the
project. They were instrumental...with a focus on
relational database & NoSQL storage, UI/UX design, security and scale.
Most recently, he's been part of a team to develop a
Platfo…
updated 10.3 years ago • Valerie Obenchain
In the directory AnnotationDbi/R, the 2 following files were modified.
sqlForge_baseMapBuilder.R:
Comment out line 234:
sql <- "INSERT INTO probe2gene SELECT DISTINCT m.probe_id, u.gene_id \
FROM min_other_rank as m INNER...the error:
RS-DBI driver: (error in statement: no such table: src.unigene)
sqlForge_tableBuilder.R
Comment out line 181:
sqliteQuickSQL(db, "ANALYZE;")
and line…
updated 16.6 years ago • Gaspard Lequeux
I have published \`RTCGA.rnaseq\` R package that provides datasets from TCGA project containig RNA sequencing (gene's expressions). I am wondering if there is a way to change this package name to be more proper like \`RTCGA.RNAseq\` and if that's possible, how should I do that and to whom should I...from TCGA project containig RNA sequencing (gene's expressions). I am wondering if there is a way …
updated 10.1 years ago • MarcinKosiński
for example I put a threshold as
padj < 0.01
log2fold\_condition1\_condition2 > 2 (Fold change of 4)
How to pass this parameter to the "plotDEXseq" function ? Shall I subset the DEXSeqDataSet object according
updated 8.4 years ago • layal8785
Hi,
I'm investigating changes in gene expression after a body weight loss intervention. The data includes baseline measurements and two follow
updated 21 months ago • jari.karppinen
The values I calculate manually for log2 fold change (using R or Excel) are always slightly different than the lfcMLE value, I'm curious why that would be (sorry, stats isn't...The values I calculate manually for log2 fold change (using R or Excel) are always slightly different than the lfcMLE value, I'm curious why that would be (sorry, stats isn't my...Condition 1 average: 20572.09809
Condit…
updated 8.3 years ago • Mike
div class="preformatted">Dear all,
I have recently upgraded my linux machine from R1.6.2/Bioconductor 1.1
to R1.7/Bioconductor 1.2 and have found that the new version...runs
considerabley slower than the old version. So much so that I have a
function to calculate fold change for an expression set that takes a
few minutes to run in R1.6.2/BioC 1.1, but well over half an hour to
run on the late…
nbsp;I have following output of DESeq2 on the following functions. It seems that if changes the fitType for dispersion only when I compute variance stabilized values. Why doesn't it change the dispersion fitType
updated 10.0 years ago • tonja.r
I have been using the following tutorial by Stephen Turner and Will Bush to look at some RNA-seq data.
http://www.gettinggeneticsdone.com/2015/12/tutorial-rna-seq-differential.html
Looking into GAGE's documentation, it looks like this tutorial is using it in a somewhat non-standard way. Specifically, it looks like they are using it to conduct a GSEA-esque analysis, feeding it a vector…
updated 8.2 years ago • JMallory
<div class="preformatted">Dear Ross,
Short answer:
The vst transformation is asymptotically equivalent to the log2, and
2^logFC is the correct transformation.
Longer answer:
See
http://www.ncbi.nlm.nih.gov/pubmed/20929874
for why vst gives small fold changes, and what you should do about it.
BTW, there is nothing "linear" about raw scale intensities for
fold-changes. The logFC ar…
updated 13.9 years ago • Gordon Smyth
Recent ...
Replies
Answer: How to install packages such as TCGAbiolinks, SumarizedExperiment?
by
Gordon Smyth
53k
The warning message is telling you that you already have the packages installed.
However, you might consider upgrading to the current vers…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
Frank
•
0
Created by French developer Julien "Orteil" Thiennot, Cookie Clicker transformed the gaming landscape by introducing a new genre of idle ga…
Comment: Empty boxes in treemap plot rrvgo package
by
TikTsokaasocissalpc
•
0
Clear visualization matters just as much in mobile entertainment as in data analysis. The [Try KK33 Game App now][1] focuses on clean layou…
Comment: nice 3D displays for PCA analysis
by
adam80haynes
•
0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
Comment: Bioinformatician at the Lausanne University Hospital
by
TikTsokaasocissalpc
•
0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
Votes
Awards
• All
Teacher to
Gordon Smyth
53k
Popular Question to
shepherl
4.2k
Popular Question to
Hervé Pagès
16k
Popular Question to
Istvan Albert
▴
50
Locations
• All
United States, 25 minutes ago
The city by the bay, 2 hours ago
Barcelona, Spain, 3 hours ago
United States, 4 hours ago
United States, 6 hours ago
United States, 25 minutes ago
The city by the bay, 2 hours ago
Barcelona, Spain, 3 hours ago
United States, 4 hours ago
United States, 6 hours ago
Traffic: 1503 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6