Hi,
How to do a GEO query using keywords in R?
I found a few publications but they use the GSE accession number:
<span style="background-color:Yellow">`` GEO_DATASETS <- ```` c ```` ( ```` "GSE73835" ```` ) ``</span...Hi,
How to do a GEO query using keywords in R?
I found a few publications but they use the GSE accession number:
<span style="background-color:Yellow">`…
Order by: Relevance
0.9618639 1.0000000
## qplot RNA-Seq
rnaseq.d0d1.qplot <- qplot(data=rnaseq,x=d0mean,y=d1mean,log="xy",
main =
"qplot RNA-Seq d0mean-d1mean")
rnaseq.d0d3.qplot <- qplot(data=rnaseq,x=d0mean,y=d3mean,log="xy",
main =
"qplot RNA-Seq d0mean...d3mean")
rnaseq.d0d6.qplot <- qplot(data=rnaseq,x=d0mean,y=d6mean,log="xy",
main =
"qplot RNA-Seq d0mean-d6mean")
## qplot microarray
ma…
updated 11.7 years ago • Willemijn van Mossevelde
Dear all,
I have performed a Differential Expression Analysis using
dds <- DESeqDataSetFromMatrix(countData = cts,
colData = colData,
design = ~ Type+ batch)
dds<- DESeq(dds)
I understand that even though I included "batch" in the formula, but I still see a batch effect.
I read this:
"Why after VST …
updated 5.2 years ago • Bine
Hello, all
I am just wondering if I am misunderstanding the consensus peak. I am under the impression that this is the number of peaks contained within a set. for example all peaks in control replicates. When using overlap the last number matches my venndiagram, but when added the consensus peak to my set it does not:
<pre>
dba.overlap(te…
updated 8.9 years ago • cperez5
P-values have "NA" values even though there are no obvious outliers in the sample transcript counts, nor multiple zeroes.
# include your problematic code here with any corresponding output
I did not get any errors running DESeq2
updated 4.8 years ago • sagharib
bioconductor.org/packages/2.3/bioc/bin/windows/contrib/2.8/AB
array_1.10.0.zip
> ")
>
>
> nor :
>
> getURL("
>
> http://bioconductor.org/packages/2.3/bioc/bin/windows/contrib/2.8/AB
array_1.10.0.zip
> ",file="target.zip
updated 17.2 years ago • Sean Davis
Tremendous opportunities for discovery are emerging in the biological and biomedical sciences, as well as in traditional physical and social sciences, but they will require the combined power of theory, data analysis, and simulation. In the biomedical sciences, for example, researchers are being confronted by an explosion of information from genome sequencing, gene expression profiling, proteomic…
updated 4.0 years ago • simonsF.careers
Tremendous opportunities for discovery are emerging in the biological and biomedical sciences, as well as in traditional physical and social sciences, but they will require the combined power of theory, data analysis, and simulation. In the biomedical sciences, for example, researchers are being confronted by an explosion of information from genome sequencing, gene expression profiling, prote…
updated 4.3 years ago • simonsF.careers
condition, time of treatment, not even \[A\].
How do you do it in edgeR?
In R, assuming the log(expression) being normally distributed, you could simply do glm(log(expression) ~ disease\_condition + \[A\] + time. Then you only...need to check the slope of \[A\] and its p-value, right? But since log(expression) is not normally distributed, we cannot use glm in R.
While in ed…
updated 8.8 years ago • mousheng xu
div class="preformatted">Dear Matthew,
I guess the main publication is my own - at present only an
unrefereed conference proceeding.
http://www.stat.psu.edu/%7Ewzhao/bcc/respapers...were a "big believer in single channel analysis of loop
>designs." Can you point me towards any publications that sway your
>opinion that way? I've always done dual channel analysis of loop
>de…
updated 20.0 years ago • Naomi Altman
<div class="preformatted">Hi All,
I am having trouble with the distinction between the functions "roast"
and "romer" in the limma package. From the publication describing
"roast" (http://dx.doi.org/10.1093/bioinformatics/btq401), it seems
that it tests a particular gene set...with the distinction between the functions "roast"
and "romer" in the limma package. From the publication describin…
One with my gmail account and one with my NIH account. Please also remove my name from showing in a public google search.
Code should be placed in three backticks as shown below
```r
# include your problematic code here with any
updated 2.3 years ago • QG
a home made RNAseq dataset, and I would like to compare the expression of some genes to TCGA samples (public data). I am not talking about differential analysis here, rather descriptive analysis.
What I would like to do is to first
Hi,
I have read through the regioneR manual and I can't find an explanation of how the y axis values are calculated for the permTestResults plot. I used numOverlap and randomizRegions for my parameters. The x axis is num overlaps. I did notice in the publication that the plots y axis was labeled as 'probability', but I am not sure exactly how the probability was generated and...numOverlap and ra…
updated 8.1 years ago • gonzalpk
to MACS2) as way of calling peaks for my ATAC-seq analysis. My output files from the Genrich are .log and .narroPeak files. Can I use the peak files in DiffBind?
Thanks!
Gayani
div class="preformatted">Hi All,
Is there a way to get the normalized log mean intensity values from
the limma analysis, and then to rank order these values from 1 to 100?
Thanks,
Chuming
</div
preformatted">
Is it possible to return intensity ratio values from marrayNorm ?
rather than the log-intensities ?
Or if not the easiest way in R to change maM to these values ?
thanks
Jason</div
updated 22.8 years ago • Jason Skelton
<div class="preformatted">Hello!
I am trying to optimize my data processing based on the addition of
ExFold ERCC controls. Ideally I would like to normalize with VSN using
the procedure in chapter 7 of the vsn vignette. If I pull out the
unprocessed intensities for the ERCC controls, order them by
increasing concentration, and transform the concentrations and
intensities by log base 2. I …
articles/10.1186/s13073-018-0567-9) with 8 high grade glioma samples. For a particular sample, I log normalize data using the method of Lun et al. (2016) and run GSVA on a subset of cells (putative cancer cells) using some gene...by this result. Do you think this could be due to the existence of outliers with extremely low log counts?
Here are the sample means for the gene set
).
`` library(flowFit) ``
`` library...logDecades using acquisition resolution<br/>
proliferationFitting: No logDecades provided. Setting LOG dynamic range from flowFrame: log decades: 3…
updated 8.2 years ago • gero.knittel
Enter the body of text here
I've tried to install DeSeq2. and received the following warnings as shown below
Code should be placed in three backticks as shown below
```
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.1 (2022-06-23)
Installing package(s) 'DESeq2'
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/contrib/4.2:
cannot open URL …
updated 3.1 years ago • hong
lt;- ncol(x)
col <- brewer.pal(nsamples, "Greens")
par(mfrow=c(1,2))
lcpm <- cpm(x2, log=TRUE)
boxplot(lcpm, las=2, col=col, main="")
title(main="A. Example: Unnormalised data",ylab="Log-cpm")
x2 <- calcNormFactors(x2)
x2$samples...norm.factors
lcpm <- cpm(x2, log=TRUE)
boxplot(lcpm, las=2, col=col, main="")
title(main="B. Example: Normalised data",ylab="…
updated 6.7 years ago • mahmudornob
interception of
this message or the use or disclosure of the information it contains
may violate the law and subject the violator to civil or criminal
penalties. If you believe you have received this message in error
updated 12.9 years ago • delhomme@embl.de
the six columns of your design matrix correspond to: Ras(Tum),
Ras1H(Tum), RasNot(Tum), Ras(Nor), Ras1H(Nor), RasNot(Nor).
Then you can make contrasts for any comparisons you are interested.
For example:
> con.matrix <- cbind
and I am analyzing RNAseq data mapped to a genome using RSEM+STAR and also only STAR.
In RSEM log the mapping percentages for one sample look like this:
```
Number of input reads | 60070942
Average input read length | 200
UNIQUE...And I also added a few more genes in the annotation and mapped again using RSEM, and the log looks the same as…
updated 2.4 years ago • vitoriastavis
BiocManager")
BiocManager::install("DESeq2")
sessionInfo( )
Session info:
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16
Matrix products: default
LAPACK
div class="preformatted">Hi,
I want to ask some questions about limma package .
if my data is not log-transform, whether also could use "lmFit"
function?
thanks!
Chang
[[alternative HTML version deleted]]
</div
However, I am not sure about following statement from the vignette:
> ... MAST assumes that log-transformed approximately scale-normalized data is provided.
In the function above raw counts are log transformed, but
updated 2.9 years ago • zuljiamel1991
DGEExact
object. I have used edgeR to produce an DGEExact output table. The
data
frame contains the log-concentration (i.e. expression level), the log-
fold
change in expression between the two groups/conditions and the p-value
updated 15.1 years ago • Karen Sherwood
res$pvalue))
head(tab)
par(mar = c(5, 4, 4, 4))
plot(tab, pch = 16, cex = 0.6, xlab = expression(log[2]~fold~change), ylab = expression(-log[10]~pvalue))
lfc = 2
pval = 0.01
signGenes = (abs(tab$logFC) > lfc & tab$negLogPval > -log10(pval
updated 9.9 years ago • John
am working on a set of affymetrix arrays, and I am interested in
obtaining the A and B values in lfc = log(A/B).
I wrote several small functions to annotate my topTable outputs, and
one of these annotations was the exprs() for each...by eBayes() and so on.
So can I take a lfc, A, M, exprs(), et cetera to get the values that
the log fold change is directly calculated from?
Sorry if this questio…
loess
normalization?
Another intriguing question (at least for me) is whether one should
take
logs prior to loess normalization. I know why one should usually take
logs
to do t-test or ANOVA analysis (to make the data look
updated 18.4 years ago • Ulisses M. Braga-Neto
Each year at TIDES, nearly 100 of the industry's top scientists give public presentations on the latest scientific and industry news on oligonucleotides, peptides, mRNAs, and genome editing
updated 20 months ago • bocsci11
Hi:
Before diving into analysis of (public) RNAseq data, I discovered that the data are stored in two BigWig files per sample (i.e. carrying a 'neg' identifier, the...Hi:
Before diving into analysis of (public) RNAseq data, I discovered that the data are stored in two BigWig files per sample (i.e. carrying a 'neg' identifier, the other
updated 3.9 years ago • bas_work
Hello,
Greetings!
I am new to RNAseq analysis and currently learning how to utilize R to determine the numbers of differentially expressed genes (DEGs) that are upregulated and downregulated. I have obtained some data from public papers, but I am uncertain about which R package to use with this normalized data. (I have attached the file.)
Could you kindly...expressed genes (DEGs) that ar…
but haven't seen a path to determine this information. It doesn't seem readily stated in the publications I've scoured thus far either.
Any help with this endeavor would be much appreciated!
Thanks
updated 4.7 years ago • rebeliscu
Bioconductor 3.11?
Nominate it for a Bioconductor New Package Award!
Nominations are open to the public and the deadline is June 15!
Please fill out the [Nomination Form](https://docs.google.com/forms/d/e/1FAIpQLSdaI6KHsezSQLWcCAzRCLlOz_fJai59PcyIz03ifutbwmXaVw
updated 5.6 years ago • shepherl
document/d/1ccXPFc_bGZoW3DgfgXf13_4i5TXySvXQCdRR8UJr__I/edit). Nominations are open to the public and any individual may submit more than one candidate; you just have to be willing to fill out the [Nomination From]((https
updated 5.6 years ago • shepherl
viewform) them by June 15. Applications are open to the public and any individual may submit more than one nomination
updated 5.6 years ago • shepherl
five multidisciplinary programmes, organised around
the
following themes: Cancer, Epidemiology and Public Health,
Cardiovascular
and inflammatory processes, Biomedical Informatics,
Neuropsychopharmacology.
The centre...candidate will be responsible
for the full cycle of microarray data analysis projects with a set of
public, licensed and in-house bioinformatics tools. He/she will
incorporate in …
updated 17.9 years ago • Robert Castelo
packages for differential transcriptome and alternative splicing analyses in large in-house and public datasets, including TCGA (10%) • Arrange and deposit NGS data to appropriate public repositories (e.g., dbGaP, GEO, etc.) upon...manuscript acceptance/publication (5%) • Implementing and/or developing publically-accessible databases to share Lab data and results with the biomedical
Hi everyone,
I just installed the new R (4.4.1) and now I get the error message "paths not writable" when I try to install any Bioconductor package. See below
```
BiocManager::install("LEA")
getOption("repos") replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager") for details.
Replacement repositories:
CRAN: http://cran.rstudio.com/
…
updated 15 months ago • gabry.scata
linear model(Ulm), you need the normalized counts. Using your example, you used the normalized log-transformed counts. In deseq2, would that be equivalent to retrieving this information from this code:
counts(dds, normalized
updated 14 months ago • James
div class="preformatted">Hi to all,
I've a doubt about Limma Package when working with log-ratios (M
columns
from MAList object) as input data.
As I don't have A columns, Can I perform the AveExpr calculation?
--
Sincerely
figure out where the variances come from**. They are not the variances of the predicted CPM values, nor are they the variances of the predicted counts when I convert back to counts (log2(CPM_pred) + log2(library_size + 1) - log2(1e6
updated 3.1 years ago • Brian
Hello Repitools developers,
I am trying to obtain % methylation values from MeDIP samples where I do not have SssI control using BayMeth, but I fail at the first step: the creation of a BayMethList object. This function results in an error if no control is provided. I found no examples of a SssI free analysis in the vignettes nor the supplementary information of the article describing the method…
updated 10.4 years ago • Matthias Lienhard
2))) # Killed after several minutes
</pre>
This doesn't happen if I set `` bigmat <- 1 ``, nor if I remove the `` stop `` call in `` .recount_cells ``. In those situations, both of the `` bplapply `` calls above execute in a timely manner
updated 9.4 years ago • Aaron Lun
A and B, in their
nomenclature) data. At that, point, I think I cannot do neither
normalization nor QC, can I? What happens if somebody tries to
normalize these signals and, for example, color balance was not
adjusted? Or does
updated 13.5 years ago • Gustavo Fernández Bayón
the following error message:
Error in if is.na(n) || n > 65536L) stop("size cannot be NA nor exceed 65536") :
missing value where TRUE/FALSE needed
Would anybody by chance know how to resolve this issue. I am also trying
updated 5.3 years ago • pthom010
Hi, I recently upgraded to latest **R 4.3** from **R 4.1**. While running the DEA workflow on scRNA-seq data, I noticed it was dramatically slower with my latest setup. I wonder if anyone are aware of changes that may have contributed to this, and how I can make the dispersion estimation step to run as fast as before?
Using a small dataset with 49 cells as demo (22 vs. 27 in two tissues), here'…
for example, typically run normalization first, whether
on one
color or two color data, then Log transformation, before statistic
analysis
(such as F-test).
Sorin Draghici, in his book of "Data Analysis Tools for DNA
Microarrays...suggested workflow for cDNA microarrays in 8 steps (p.337). Log
transformation is the step 7, after several normalizations.
R package "IlluminaGUI" does quantile nor…
updated 18.6 years ago • Longsi Ran
values are calculated by log2(TPM_exp+1)-log2(TPM_control+1) [using 1 or 0.5 as pseudo counts for log transformation]. In my case, I realized that TPM is not a good way to normalize the data as I have few samples with lot of reads...transformation of the normalized counts. By doing this I believe I can also reduce the inflation of log fold change values for genes with small counts. If this is oka…
updated 3.0 years ago • Jayesh Kumar
plot with labels.
<pre>
plotMA(data.fit.eb, coef = "IVIgiTreg_vs_n_iTreg", xlab = "Average log-expression", ylab = "Log Fold Change", main = "IVIg_iTreg vs n_iTreg")</pre>
This gives a plot without labels, and I am not sure how to...extract the coordinates of those genes that are most differentially expressed (e.g. the top 20 log fold-changes)?
The plot ima…
updated 10.5 years ago • Gabriel Nathan Kaufman, Mr
100%
loading from cache
> xtgenome <- ensembldb::getGenomeTwoBitFile(xtah)
snapshotDate(): 2022-10-31
Error in .local(x, ...) :
No genome assembly fasta file available for organism: Xenopus tropicalis, data provider: Ensembl...and genome version: Xenopus_tropicalis_v9.1!
```
```r
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running …
updated 2.3 years ago • cjag
with
fit <- lm.series(exprs(E), design)
My question is:
Is the data in E supposed to be on a log scale (like after using vsn)
or not?
Thanks for your help,
Julia</div
shall I do now?
#
# Social Network Login Failure
An error occurred while attempting to log in via your social network account
updated 10.4 years ago • MarcinKosiński
adj.P.Val), pch = 20, main = "Volcano", col = "grey",
cex = 1.0, xlab = bquote(~ Log[2] ~ FC),
ylab = bquote(~ -log[10] ~ P ~ value)))
with(subset(topT, adj.P.Val < cut_pvalue & logFC > cut_logFC),
points(logFC, -log10(adj.P.Val
updated 2.9 years ago • Sooni
Rb="B635 Mean",Gb="B532 Mean"))
dat <-normalizeBetweenArrays(RG, method="quantile")
> dat2 <- log (dat)
*Error in log(dat) : Non-numeric argument to mathematical function
*rownames(dat@hx) <- RG.final$genes$Name*
Error in rownames
EC.data, bRetrieve=TRUE)
But the values I can see are not corresponding to the peak -log(10)pvalue that was in the narrowPeak file, it seams to have been normalized, can you please explain me how this normalization...is done?
I thought the -log(10)value from the narrowPeaks file was directly begin used by default.
Thanks
Alejandra Medina
&nb…
updated 11.0 years ago • medinaale
background is higher than the spot (i.e. no gene detected) it gets
a
negative value.
Needless to say, log-transformation is not working on these.
So therefore I came up with an alternative to make log-transformations
work.
I replaced
Recent ...
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Comment: Guitar R package requires update due to dependency GenomicFeatures
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ferran.llobet.cabau
▴
10
Thank you @seandavi for your feedback.
I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
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★
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…
Comment: Ensembl plants at annotationHub?
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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
by
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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