that the variance is stabilized, I believe I could directly use limma to asses the significance of changes on the peptide level. However, I would like to have a model for the significance on the protein level, which takes into...quite variable) and assigns higher significance to proteins with several peptides showing consistent changes than with just a single peptide showing the same change.&…
Order by: Relevance
I am using `` ReportingTools `` in conjunction with `` DESeq2 `` to create a standard HTML report of differentially expressed genes using the recommended syntax for object class `` DESeqDataSet ``. Everything works fine except the default plots use a log10 scale and autozoom. I would like to create a linear scale with a fixed origin of 0 for all counts.
Initially I thought of passing a…
updated 7.3 years ago • trebbiano
img alt="P-values before" src="https://image.ibb.co/kN0nU5/pvalue_dist_deseq.png" style="float:left; height:218px; width:378px"/>
<img alt="After FDR correction" src="https://image.ibb.co/dQfzbk/after.png" style="float:left; height...some underlying hidden effect, maybe a batch or lane effect? I'll need to get these data from the source.
Thanks.
Thyago
updated 8.4 years ago • tcalvo
Hi I have some questions about the shrinkage of log2 fold changes:
Is it always useful or in some cases is it advisable to disable it?
Are there plots helpful to show when use it or not...Hi I have some questions about the shrinkage of log2 fold changes:
Is it always useful or in some cases is it advisable to disable it?
Are there plots helpful to show when use it or not?
The
updated 5.0 years ago • ribioinfo
which peaks are being shuffled? the query or the target peak? How the p value is a computed? The source code would be helpful here.
When I interchange the query and target peaks, the output are totally different, could change...The same two peaks, just depend on which is feed into the query versus the target, the result changed completely. I would appreciate your insight on this issue. since thi…
updated 7.5 years ago • majingqun
<div class="preformatted">Hi
Firstly, I think limma is excellent and use it a lot, but some recent
results are a bit, erm, disappointing and I wondered if someone could
explain them.
Basic set up was a double dye-swap experiment...div class="preformatted">Hi
Firstly, I think limma is excellent and use it a lot, but some recent
results are a bit, erm, disappointing and I wondered if so…
Hi everyone!!
I´ve recently installed Bioconductor and run it this way:
<pre>
<strong>source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite
updated 10.7 years ago • dany_wm44
<pre>
Hi, I am trying to install Bioconductor and I would like to have all the packages updated. What should I do I already updated the R packages.
Thank you for the help
Here is my code
update with biocLite()
Error: 6 package(s) out of date
> try http:// if https:// URLs are not supported
Error: unexpected symbol in "try http"
> source("https://bioconductor.org/b…
updated 7.3 years ago • jpenadi1
Hi Everyone,
I recently had to reformat my mac to get the OSX Yosemite. Now I run into the problem that the oligo package does not work.
The reason...http://www.affymetrix.com/catalog/131444/AFFY/HT+MG-430+PM+Array+Plate\#1\_3</a>
Any comments/suggestions are welcomed. I am on the brink of trying figuring out how to build my own annotation package from here
updated 10.3 years ago • peer.karmaus
Hi everybody!
I would like to know if there is a way to change stringtie "gene_id" with "ref_gene_id" when performing featureCount to construct the count table for edgeR.
The thing...named genes. I would like to know if using an option in featureCount gives the posibility to change from gene_id to ref_gene_id that is the ENSMBLE ID.
Maybe -g < string > (GTF.attrType), …
updated 7.0 years ago • IRAIA.MAIALEN
Hi
I´m using plotBCV which has a legend included in the top-right corner of the plot. I would like to change the names in the legend because when I reduce the size of the plot to export it to pdf, the names in the legend goes out of...I´m using plotBCV which has a legend included in the top-right corner of the plot. I would like to change the names in the legend because when I reduce the size of…
Charles-23991`, and importantly its link to my GitHub account, into `7857`, which has all of my past history ?
Thanks !
-- Charles
updated 4.4 years ago • Charles
Hi All,
Just share a recent experience with installation. I'm a beginner of bioinformatics (trained on the experimental side of genetics). Hope...it is useful for other newbies like myself.
I recently set up ubuntu 14.04 and updated R to the newest version through CRAN. Then got problems installing packages. Below...by regular startup of R (not through sudo R).
Honestly, I'm still a …
updated 10.5 years ago • doublehelixlf
color:rgb(229, 233, 236)">If you are a user of biomaRt (a part of the Bioconductor library) change the host from 'www.biomart.org' to 'www.ensembl.org'. </span><span style="line-height:1.6">"</span>
> listMarts(host='www.ensembl.org...6: Premature end of data in tag html line 2
<span style="line-height:1.6">Does anyone know how to change the host?&…
updated 10.2 years ago • Cheng-Yuan Kao
__ Do not manually pass `` txi$counts `` alone to downstream methods, if you have left `` countsFromAbundance="no" ``. This is simply passing the summed estimated counts, and does not correct for potential...packages/3.7/bioc/vignettes/tximport/inst/doc/tximport.html#rsem)
But when i try to change the __countsFromAbundance__ parameter of func…
4000 reads per sample and time point. For comparison, I'm showing below the log2(cpm+0.01) on the left for 4 genes and the voom normalized data in v$E for the same 4 genes on the right; it's the gene in the bottom left of both plots...twice, once in infected and once in control).
Are there any explanations for how voom would change the sign of an effect like this compared to the cpm data? Thank…
updated 4.3 years ago • taur.vil
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3269.html). Essentially they look for changes in exon reads between two samples and changes in intron reads between two samples and classify transcripts as post...transcriptionally regulated when there is a discrepancy between changes in exons and changes in introns.
They use a linear model ~ region + condition + region:condition…
updated 10.5 years ago • Jake
I'm new to both R and DESeq2 and I have a script to work off but this will only generate Log2 fold change? Does anyone know what script to add to calculate untransformed fold change to my read counts?
I've attached the script...on the object dds27
dds27 <- DESeq(dds27)
#here results are generated and saved as res27, can change p-value cut off by changing alpha value
res27 <-…
are barcode sequence not with specified length.
It is true my barcode length is 6 not 5. How can I change this on edgeR? I can't seem to find the script that I can edit anywhere on the edgeR program/folder.
Thanks
updated 9.7 years ago • lucia.caceres
50 or more warnings (use warnings() to see the first 50)
></pre>
I therefore would like to set/change the location where this SQLite file is stored.
Since I am working on a Win7 machine, I changed the "start in" directory of...to a local dir (from "M:\\My Documents"), but this did unfortunately not solve the problem. Idem for changing the Win7 "Environment Variables" (System prope…
updated 10.2 years ago • Guido Hooiveld
here
Hello,
I am trying to do secondary research on published data that lists only the fold change in genes between 2 stages for 2:3 different tissue types without any further analysis. I am trying to apply the protocol...any advice on how to estimate the dispersion and continue the analysis, starting from the log change and not gene counts. I understand that edgeR from documentation specif…
updated 4.6 years ago • Manal
However there are no replicates; only one case and one control.
I want to plot how the Log2 Fold change is correlated between the two
data sets as they are looking at similar samples.
The microarray data is easy as Limma...reports log2 fold change but NGS
on the other hand does not.
What would be the best package/approach to generating a log2 fold
change of the next
updated 14.5 years ago • john herbert
<div class="preformatted">Hi there,
Just packaged BSgenome.Rnorvegicus.UCSC.rn5 (Rat) and
BSgenome.Ggallus.UCSC.galGal4 (Chicken), and dropped them
into our BioC 2.11 (devel) repository. They should become
available via biocLite() within the next hour or so. Note
that only the source tarballs will be available for the moment
so Windows and Mac users will need to install with:
install.p…
<div class="preformatted">I am having trouble reading the Agilent arabidopsis 22575 gene array
using
read.maimage in Limma under R 2.1.1 (I don't know the limma version,
but I
just downloaded using the R packages interface, and also used the
update,
so I presume this is the most recent.
Under R 2.0.1, there was no problem reading all the data in the arrays
using:
RGf=read.maimages(c("2792…
updated 20.5 years ago • Naomi Altman
Hi all,
I am using the unique(x) function with a DNAStringSet in one of my own
functions. Recently my function has started returning an error, and I
am not sure what changed. The same line of code works fine in the R
Console
updated 15.8 years ago • Erik Wright
Hey Adi,
i have used spia a copule of time now and i never got this error before but just recently i am having this error, all my data looks very fine to me at every step but when i try running spia i get this error message.Although...all = ALL\_Colorectal, organism = "hsa", :
de must be a vector of log2 fold changes. The names of de should be included in the refference a…
updated 9.6 years ago • saamar.rajput
<div class="preformatted">
Dear All,
I have recently started (trying) to use xmapcore for analysis of my
mouse Exon 1.0 array data. Now that the install is complete, I am
having...div class="preformatted">
Dear All,
I have recently started (trying) to use xmapcore for analysis of my
mouse Exon 1.0 array data. Now that the install is complete, I am...I have managed to find are from the
…
to be random, so that very few genes
would have a d.e. call. I know that my conditions produce changes,
because I can see 1000 d.e.g on some of the comparisons, but can
really "day" produce more changes than my experiment...Thanks in advance for your comments,
David
</div
that this would indicate that HiA is set as the reference (since it is the level farthest to the left after "Levels:") and if a comparison between HiA and LoA produce a log2 fold change value that was positive, this would indicate...HiA. Is this correct? Or does relevel() always have to be done? In the case study, mock is to the left in the first table in section 4.6.4, but then also set with rel…
updated 10.6 years ago • Ekarl2
dba.count(Diff_dba, minOverlap = 2)
Diff_dba_contrast <- dba.contrast(Diff_dba_counts, categories = DBA_TREATMENT, minMembers = 2)
Diff_dba_analyze <- dba.analyze(Diff_dba_contrast)
Diff_dba_report <- dba.report...reasonable, but then the Fold values are completelly off, near 0, which would mean a near 1 Fold change, which is clearly not what the Conc values suggest. I rea…
<div class="preformatted">So, I wrote a few weeks (months, maybe) ago asking about databases.
IoBion and VisXlabs products seem to be options in the "low cost"
expression array facility category.
However, I've spent the last 3 hours (with numerous unscheduled
interruption by little ones) installing/playing with...IoBion and VisXlabs products seem to be options in the "low cost"
expression …
bump
the
> development versions? I'm not sure if this has been fixed in
Biobase,
> but the comment in zzz.R seems to indicate that's the original
source
> of the code.
>
> Thanks,
>
> Cyrus
>
> _______________________________________________
updated 20.7 years ago • Seth Falcon
existing methods have been integrated into it.
You may access it through the commands:
> source("http://bioconductor.org/biocLite.R") # R >= 2.10.0
> biocLite("DEGseq")
Comments, questions, etc, are all welcome.
Best regards
updated 16.3 years ago • Likun Wang
experimental (i.e. "R") intensities by a small factor, and asking what
proportion of these simulated changes limma detects. Does this sound
reasonable? Is there a better way?
John Welsh
Associate Professor
Sidney Kimmel Cancer
updated 21.5 years ago • John Welsh
sort of a transient issue with HEAD?
BiocInstaller version 1.1.28, ?biocLite for help
* installing *source* package VariantAnnotation ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ls...life is.John
von
Neumann<http: and.ac.uk="" biographies="" von_neumann.html="" www-groups.dcs.st-="" ~history="">
[[alternative HTML version de…
Hi everybody,
I didn't use the waterfall function from GenVisR for several months and while re-using it now the mainDropMut option did not work anymore (no error messages were displayed). If set to 'TRUE' the legend still displays all mutation types (but I do want to discard the unused ones).
As a first step I wanted to update to the most recent version, so I had to install R 4.2.0 in order to …
updated 3.6 years ago • Michel
according to CPM.
The reasons are:
1. Filter all the genes with zero counts: If zero counts are left, it turns -Inf after log2 transformation. It's really bad for future analysis. log2 are considered as a biological relevant...change. It makes no sense to do log2(counts +1).
2. I should filter out genes by considering 24 samples together. Since the gene expression
After removing genes that are not
expressed at >= 0.2 cpm in >= 5 samples I have ~600 rows left. I tried
calculating the tagwise dispersion estimate with:
cds1 <- estimateTagwiseDisp(cds1, prior.n=2, trend=TRUE,
prop.used...a very large dynamic
range). Is it possible that I am over-fitting the estimate? Would you
recommend changing any other parameters?
Best regards,
Helena…
none of them gave me
certainty. Therefore, I go to ask again, because I still have doubts.
Fold Change is the ratio between Treated (T) and Control (C). Correct?
Third question: In the majority of the cases, the data are transformed...into log in base 2. Then, in these cases, I have: (Log2 T / Log2 C).
Correct? In this case, Fold Change would be equal to 2^(Log2 T / Log2
C). OK?
Fourth question…
I am currently doing DESeq2 analysis, and I am getting opposite log2 fold change when I plot on Volcano plot.
For example, one of my genes is down-regulated (with significant p-value) according to DESeq2
updated 6.9 years ago • leekun4
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 (With R 2.2 and Bioconductor version 3.1):
ensembl\_mart\_81 <- useEnsembl...Mouse assembly updated from GRCm38.p3 to GRCm38.p4
A complete list of the changes in release 81 can be found at&nbs…
<div class="preformatted">I've been using Efetch to get some full text articles from Pubmed
Central, which works fine...
url <-
"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=PM
C2784878"
x<-readLines(url)
doc <- xmlParse(x ) # requires XML package
xpathSApply(doc, "//abstract", xmlValue)
[1] "The majority of all genes have so far been i…
updated 13.7 years ago • stubben
Hello,
The topic of this email looks easy enough, but I cannot find in the Limma documentation how the (log2) fold changes are actually calculated.
As you probably now, Limma uses log2-scaled input (originating from e.g. RMA). So, if you want to calculate a log2 fold change, it is possible to keep this log2-transformation into account or to discard it. What I mean with this is that the mean of.…
updated 8.8 years ago • Groot, Philip de
<div class="preformatted">Chris,
Thanks for your kind comment!
The following code snippets should do.
FeatureIDs = annotatedPeak[!is.na(annotatedPeak$distancetoFeature) &
abs(annotatedPeak$distancetoFeature<5000000),]$feature
library(org.Hs.eg.db)
EnrichedGO = GetEnrichedGO(featureIDs, orgAnn="org.Hs.eg.db",
maxP=0.01, multiAdj=FALSE, minGOterm=10, multiAdjMethod="")
Best…
updated 15.0 years ago • Julie Zhu
wrote:
> Hi Mark,
>
> I have been using your package (and limma) for analysis when we
> recently tried to compare it to Illumina's approach.
> One thing we were surprised about were huge differences in the
> reported...find more genes
> - are these reliable or is a more conserative approach advised?
>
> Your comments will be apprecia…
The following ONLY affects the web interface to our mailing lists.
This is both for subscription changes and the mailing list archives.
For a long time, our "Statistics ETHZ" home page has been
available both as
http://www.stat.math.ethz.ch...me, but that
should be very temporary).
For existing mailing lists and their web interface, the change
change has to happen ``inside mailman'' (by ca…
updated 21.4 years ago • Martin Maechler
gt; have worked quite systematically on this, and I would
> recommend looking at one of their recent papers:
>
> Monitoring global messenger RNA changes in externally
> controlled microarray experiments. van de...LIMMA gene-wise fdr
> corrected
> >> p<0.001) we get c.30% of transcripts on the chip changing!
>
> You are t…
updated 21.3 years ago • Matthew Hannah
I wanted to highlight a recent<sup>1</sup> change in the `` dplyr `` package that is
likely to break a lot of people's existing code. That package now exports
I use EdgeR since a while and I have noticed recently that the common dispersion estimated using estimateGLMCommonDisp() was slightly varying according to the row...the count input (gene ID order). If I do the same analysis with exactly the same input table but by changing the row order, e.g. genes ordered by either decreasing or increasing mean of count across samples, I obtain slightly
updated 6.3 years ago • hz_67
div class="preformatted">When I received a letter about recent changes I try to update
Bioconductor packages, but I get the following error message:
> update.packages(CRAN=getOption
updated 21.7 years ago • Vitalina Komashko
tagMatrixList, xlim=c(-3000, 3000), conf=0.95,resample=500, facet="row")
```
1. How do I change the labels from "Peak1,,,Peak2..." to my sample names
[1]: /media/images/c6d82200-b155-4642-a49a-73704734
Thanks
updated 2.2 years ago • inna.gur
The DESeq2 results table provides the fold change for each gene, but is there a way to get the confidence interval for each fold change the program generates
updated 4.2 years ago • adeler001
called org.Hs.eg.db for enrichment analysis, but I always met kinds of problems. The following is my recent one---package org.Hs.eg.db error.Can somebody provide a quick fix? Thanks!!
```
> if (!requireNamespace("BiocManager", quietly...3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
Installing package(s) 'org.Hs.eg.db'
installing the source package ‘org.Hs.eg.db’
trying URL 'https…
updated 6.3 years ago • ccklily
set up, that I don't seem to be handling well: whatever I do I have a relationship between the fold change and the average expression of the genes.
I have 5 main variables:
- Cell type: stem or differentiated cells
- Group disease...is the bigger the logFC is, while I expected that the average expression would affect the fold change.
I tried changing the design to a more simple one…
updated 6.2 years ago • Lluís Revilla Sancho
comparing samples, obviously the relative positions
of the 2 peaks may influence observed expression changes. Would such
peak shifts be more likely in divergent samples, and if anyone wants
to
comment on those.... ;-)
This example is
scrolling, e.g. for reading on tablets</span>
<span style="background-color:transparent">Track changes functionality? </span>
<span style="background-color:transparent">For non-technical collaborators:</span>
*
<span style...background-color:transparent">How to annotate comments in the rendered PDF or HTML file and feed them back into…
the design matrix. Could anyone give some suggestions? The data looks like this,
<table align="left" border="1" cellpadding="1" cellspacing="1" style="width:500px">
<tbody>
<tr>
<td>Sample_Name</td>
<td>Condition</td>
<td>Pair_Name</td>
<td...Source</td>
<td>Days</td>
</tr>
<tr>
<td>Sample1<…
updated 7.2 years ago • yuabrahamliu
step)
I seem to remember a paper that showed that T-tests did not predict
known spiked-in changes better than simple fold change until one had 8
or more replicates.
Is there data with known spiked in datasets (or a consensus...that
limma or sam/siggenes performs better than straight fold change with
such low replicate analysis?
Sincerely,
John Luckey</div
updated 21.7 years ago • Luckey, John
Hello,
I've recently upgraded my R version to 3.5.1, and I since them I'm having a lot of problems to install bioconductor packages: ...gt;source("https://bioconductor.org/biocLite.R")
>biocLite()
Installing package into ‘\\\\icnas1.cc.ic.ac.uk/hrb08/R/win-library
updated 7.5 years ago • AR3513
the first line is between 10,000 and 10,0039, the second line is 10,039 and 10,040. I want to change the interval to 1000 base pairs for each line and take the mean of mappability value for that interval.
Let's say: Input
updated 4.0 years ago • the
Recent ...
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