Hi all experts,
I have used Trinity software for doing de novo transcriptome assembly. Then, I used bowtie and RSEM within Trinity package for read mapping and counting. Finally, I got the raw count and FPKM value. I used raw count for doing differential expression analysis by edgeR software, say, I compared A-B library. I found that among DEG genes reported by edgeR software, some few genes wit…
Order by: Relevance
Stimulated.0.F)-(Stimulated.3.M-Stimulated.0.M)”).
However, when comparing the results (log foldchanges) from the analysis between the females and males and for males and females separately I realized something...strange (?). Sometimes the log foldchange is namely very similar in females and males for a particular gene, but still this gene has a significant value...and high log foldchange value …
updated 8.2 years ago • elinorjax
edit 2022-07-26: put complete session log, add results from other examples and remove speculative bits.
(I feel bad for the walls of...s no way to fold code here?)*
I can't get bigWig import to work with `rtracklayer`.
A full session log, using the 3 first lines of `?import.bw` examples, with `traceback` and `sessionInfo`:
```
> library("rtracklayer")
Loading required...BigWig", ...)
2:…
updated 3.5 years ago • bonob
experiments return the same trend. But I realized that the size normalization assumptions are being violated, and when I look at the size normalization factors compared to the percentages, it makes a very nice slope, which is
updated 5.3 years ago • swbarnes2
Applications are invited for the post of Bioinformatician Research Fellow to undertake a leading role in the next generation sequencing Pan-Prostate Cancer Group Initiative (http://panprostate.org) in collaboration with Dr Daniel Brewer and Professor Colin Cooper.
The Pan-Prostate Cancer Group Initiative is a collaboration of multiple major prostate cancer centres across the world designed to…
updated 5.5 years ago • Daniel Brewer
see the details of position at [https://www.zintellect.com/Opportunity/Details/EPA-ORD-CCTE-GLTED-2022-12][1].
[1]: https://www.zintellect.com/Opportunity/Details/EPA-ORD-CCTE-GLTED-2022-12
updated 3.1 years ago • whduke
soybean seeds after 24 h imbibition.
I noticed in the documentation that glmTreat uses unshrunk log-fold-changes to calculate test statistics. Both shrunk and unshrunk logFC are reported. Most of the unshrunk logFC have...8577
NotSig 25177
Up 14190
# use glmTreat to narrow list of DE genes, using a cutoff of log FC=1
tr.dead.v.dry <- glmTreat(fit, coef=2, lfc=1)
# see how thi…
updated 6.2 years ago • flemi221
DESeq2.html#quick-start
In the guide, it says to use contrast (or name) because contrast sets the log fold change to 0. I have two conditions treatment and control. And for my dds$condition, I releveled it so that the ref = "control
<div class="preformatted">Dear all,
I have a general question about whether TMM normalization is
appropriate
for my data. I apologize for this long winded email. I am not a
trained
bioinformatician and therefore have been struggling with some data
analysis.
A colleague and I did an RNA seq experiment with 6 samples (each had
RNA
pooled from 6 individuals) and no biological replicates. The …
updated 11.3 years ago • Ni Feng
div class="preformatted">We have evaluated the methods in Lumi using the MAQC benchmark data.
The publication is under review.
Pan, can you add the inter-lab concordance comparison results (Three
curves: raw, Beadstudio, and...as you may know for sure, this treatment create
negative values, because of bg subtraction, after log transformation,
I have
NaN value, when I run a simple ttest analys…
updated 18.6 years ago • Simon Lin
digest 0.6.28 2021-09-23 [2] RSPM (R 4.1.0)
distributional 0.3.0 2022-01-05 [1] RSPM (R 4.1.0)
dittoSeq 1.7.0 2022-02-10 [1] Github (dtm2451/dittoSeq@b158b29)
doParallel 1.0.17 2022-02-07 [1] RSPM (R 4.1.0...ggbeeswarm 0.6.0 2017-08-07 [1] RSPM (R 4.1.0)
ggdist 3.1.0 2022-02-13 [1] RS…
updated 3.8 years ago • tangming2005
detected and on the low interquartile range of
intensities. Fig. 2 from PMID23136189 (admittedly my publication)
shows
the range of IQRs for samples within several published studies using
Illumina BeadArrays for FFPE tissues...beadlevel_data, transFun = logGreenChannelTransform, col =
"green",
> ylab = expression(log[2](intensity)), las=2, outline=FALSE,
> main= "Array inte…
Is there an alternative constructor to create a gate from real
dimensions?
2) Plotting on a log scale
Currently I'm transforming my "Log" data with a log?? transform:
flowset <- transform(flowset, `SS.Log` = log10(`SS.Log`))
flowset...lt;- transform(flowset, `FL.1.Log` = log10(`FL.1.Log`))
When plotting, I have the log values on the axes. However, is
it possible to either:
a) plot …
updated 15.3 years ago • Roger Leigh
do not have any *a priori* reason to believe that openness would tend to decline in this comparison, nor do we have any reason to believe that there would be few or many significantly differentially open regions (we observe...efit, column=1, status=abs(eres[,1]), main=colnames(efit)[1], ylab="log2(fold-change)", xlab="Mean log(CPM)", legend=FALSE, cex=0.5)
abline(h=0, col="darkgrey")
…
interception of
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may violate the law and subject the violator to civil or criminal
penalties. If you believe you have received this message in error
GAGTTGTTGC TTCATGGAAC"
[5] "Bar ---TTATTGT TTAGTCTGCA G-TCACAGTA GAGTTGTTGC TTCATGGAAC"
[6] "Nor AGATTATTGT TTAGTCTGCA G-TCACAGTA GAGTTGTTGC TTCATGGAAC"
[7] ""
[8] "Oki CGGGCTGCTG TAAATCAGAG GACTCGGTCT CGGCCGAGCG CGCGCTGACC...CGGACGAGTG CGCGCTGACC"
[11] "Bar CAGCCCGCAG TAAATCAGAA GACTAGGTCG CGGGCGACTG CGTGCTGACC"
[12] "…
updated 3.9 years ago • Charles Plessy
Dear bioC,
How can I use a github (not CRAN) dependency in bioconductor package?
I added in DESCRIPTION
Remotes:
github::vnijs/MathJaxR (>= 0.11)
but does not work.
Karim
Thanks
updated 10.0 years ago • kmezhoud
Install for IPO and msdata both fail, with a simple "lazy loading fails" message (IPO shown below)
I thought maybe one of the dependencies was missing, tried to run xcms, but whenever I call the library, R shuts down unceremoniously.
Any ideas for a fix?
```r
sessionInfo( )
BiocManager::install("IPO")
library(xcms)
```
# 1: session info
R version 4.2.0 (2022-04-22 ucrt)
Platf…
<div class="preformatted">Greetings,
I have been trying to find a quantitative measure to tell when the
data
distributions
between chips are 'seriously' different enough from each other to
violate
the
assumptions behind quantile normalization. I've been through the
archives
and seen some discussion of this matter...tell when the
data
distributions
between chips are 'seriously' different en…
updated 21.8 years ago • Stan Smiley
and also associated with traits seem physiologically relevant. I am not going to get around, nor would I want to get around, reporting the confounding effect, but what are the best practices for reporting putative "real...supplement, but I want to be forthright in the narrative as well wherever I present the data before publication.
Thank you for your time
updated 6.9 years ago • cats_dogs
so that each host plant species is replicated in each soil treatment. I think an estimate of the log-fold changes (LFCE) associated with soil treatments and host plant species would be informative. Basically, which...samples labelled Species 1 to all other samples in my dataset, basically for each feature estimate log fold change between mean of Species 1 and grand mean. I can repeat th…
that the sequence depth is different between WT and CKO samples.
I checked the "regularized log transformation" part of the vigentte as well as the original paper of "DESeq2",
To be honest, I was not able to fully understand
researchers and external collaborators in the planning, analysis, interpretation, presentation and publication of diverse NGS and other omics data sets
- Contribute to the development of data analysis workflows and pipelines...for two years with an option for permanent employment
**Application Deadline:** January 16, 2022
### Declaration of Consent and Data Protection
By sending us your appli…
updated 4.1 years ago • sergisayolspuig
the values
\delta
> h for differential expression (equivalent to the difference between
the
> log-ratios if using rma()) are both on the wrong scale. Well, as
rma()
> and other methods use log-transformed data, but vsn() uses a
different...gt; tranformation, I think using expresso() to calculat vsn-normalized
> measures seems to log- AND arcsin-transform the data. Is t…
updated 23.0 years ago • Dick Beyer
to The Carpentries lesson about the Bioconductor project
**When:** Thursday 20 October 2022, 11am EDT, 4pm BST.
**Register:** https://www.meetup.com/boston-r-bioconductor-for-genomics/events/289042169/
**What:** Let the community...know about your activities on the biocblog.
**When:** Wednesday 26 October 2022, 9am ET, 2pm BST, 10pm JST.
**Register:** https://www.meetup.com/bioconductor-…
updated 3.2 years ago • Maria Doyle
is shown as a black curve (axis on the right)". In my case, I do not see either the coverage curve, nor the axis on the right.
best,
Antón
updated 10.9 years ago • antonvila.s
of certain categories in non-significant genes. However, I am not sure whether this doesn't violate some assumptions in the underlying statistics, so I would prefer to just do a proper two-tailed test.
Is this possible
effects, but I'm finding a very large number of DEGs. In this case, I'm unsure if my data set violates any assumptions for TMM, how robust TMM might be to these violations, and what consequences are to be expected. I'm using
updated 7.0 years ago • rproendo
Treatmenttime.C.T._trt1day_vs_ctrl1day"))
which is giving me a log P values of "Genotype.S.R._Susceptible_vs_Resistant_vs_Treatmenttime.C.T._trt1day_vs_ctrl1day"
But I am trying
May I know how do I fix this? I'm currently using R4.2.2 on MacBook Air, M1\
R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"\
Copyright (C) 2022 The R Foundation for Statistical Computing\
Platform: aarch64-apple-darwin20...CRAN: https://cran.rstudio. com/
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31)\
Warning message:\
package(s) not installed when versio…
updated 3.1 years ago • laujihen
intervals. I have
3 wild type samples, 3 MUT samples and 3 drug treated samples
```
WT1 - 12/14/2022
WT2 - 12/14/2022
WT3 - 11/03/2021
MUT1 - 11/03/2021
MUT2 - 11/03/2021
MUT3 - 11/03/2021
DRUG1 - 11/03/2021
DRUG2 - 12/03/2021
DRUG3 - 11/03/2021
updated 3.4 years ago • gv
none",
metrics=FALSE)
# Creation of summary data
BSData39A <- createBeadSummaryData(BLData39A, log=FALSE,n=3,
imagesPerArray=2)
BSData39B <- createBeadSummaryData(BLData39B, log=FALSE,n=3,
imagesPerArray=2)
BSData39C <...createBeadSummaryData(BLData39C, log=FALSE,n=3,
imagesPerArray=2)
BSData39D <- createBeadSummaryData(BLData39D, log=FALSE,n=3,
imagesPerArray=2)
BSDat…
Silver ira](https://newsdustbin.com/2022/07/19/silver-ira
updated 3.3 years ago • dohow66966
of upregulated (12%) and downregulated (12%) genes acceptable in DESeq2 analysis? Does it not violate the usual result?
(2) Also, I observed that LFC > 0 and LFC < 0 automatically appeared in the result by default. As most
updated 15 months ago • madivinakristidiscar
or distribution of this e-mail or use of information contained
herein is strictly prohibited and may violate rights to proprietary
information. If you are not an intended recipient, please return this
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updated 21.2 years ago • SHMA Shaukat Mahmood
<div class="preformatted">Hello,
I'd like to solicit some advice regarding normalization of two-color
arrays in which one sample is a reference pool. These arrays may
violate the assumption that M~1 for most spots, and thus I am unsure
of
how best to correct the spatial and intensity biases that...normalization of two-color
arrays in which one sample is a reference pool. These arrays may…
updated 18.8 years ago • Oliver R. Homann
the order? As I understand,
the
hierarchical clustering will break the original order if it "violates"
the
clusters.
Thank you!
Best regards,
Lina Hultin Rosenberg
________________________________
Lina Hultin Rosenberg
updated 19.3 years ago • Lina Hultin-Rosenberg
<div class="preformatted">Hello,
I am using affy package of Biconductor.I have given raw cel
files
as input for normalization. I have to do background correction and
normalization of these files.
I am using the following commands:
> library(affy)
> Data<-ReadAffy()
> est<-rma(Data)
Background correcting
Normalizing
Calculating Expression
Warnin…
updated 15.8 years ago • Priyanka Jain
following command BiocManager: install("pheatmap") , we got the following error (sample of error log below). In the end, and despite the error gives no good clue for the real problem, the issue was that we are using Netskope for...setting that needed alteration to make these actions smoother and safer from our end.
Error log got:
Replacement repositories:
CRAN: https://cran.rstudio.com…
updated 2.5 years ago • Albert
anova, and was wondering if this screws up the
results, since the assumption of equal variance is violated (quite a
lot, I think!).
Does it make sense to "fake" a random block design by taking the mean
of the technical replicates
trying to get a png image under linux.
The problem is, that the program can't find neither savePlot() nor
png().
Does anyone know how I can save a png file?
THX,
Assa
--
Assa Yeroslaviz
L?tzenerstr. 15
51373 Leverkusen
</div
updated 20.2 years ago • Assa Yeroslaviz
and I've noticed that some functions, such as voom and cpm, don't seem to accept an offset matrix, nor do they use an offset matrix if it is present in the DGEList object. Is this an oversight or is there a specific reason that
<div class="preformatted">Hi,
I tried to install the new version 1.4, however, noticed that neither
the default (getBioC() ) nor explicitly calling getBioC("cdna") would
install the vsn library. That is confusing as the installation
instructions say...Hi,
I tried to install the new version 1.4, however, noticed that neither
the default (getBioC() ) nor explicitly calling getBioC("cdna") w…
I am trying to install Herper and it says it is not available for my version of Bioconductor. However, the Bioconductor website says that Herper should work with version 3.15 and R 4.2.1 which I have!
Here is my code:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Herper")
And here is the error I get:
&g…
mathematics, medicine, or other related fields, obtained before the start of the position (August 2022). The successful candidate will have good problem solving, troubleshooting, and analytical skills. In addition, the candidate...Application and selection process: Candidates are invited to apply online starting January 3, 2022 and submit an application no later than February 6, 2022 at 23:59 Eas…
updated 4.0 years ago • Alyce
question is : how to make the gating automatically by flowsom, because I don't have a manual gating nor an original gating. so I will need to know is there a way to make the gating via flowsom algorithm
an other question please
updated 4.5 years ago • ismail.ameran
readMSData function on it, only the TIC en rtime are being extracted, but not the single ions' mz nor their intensity.
Is it an issue with netCDF files or is there a way to get those informations ?
Best regards,
Julien
I have a data set in which the rlog transformation produces in one condition a few genes with very high log-transformed counts. Here is a mimimal example (the real data set has more gene but the same problems):
<pre>
library("DESeq2")
library...a data set in which the rlog transformation produces in one condition a few genes with very high log-transformed counts. Here is a mimimal exampl…
NA
Nb of transcripts: 40735
Db created by: GenomicFeatures package from Bioconductor
Creation time: 2022-12-06 16:31:04 -0600 (Tue, 06 Dec 2022)
GenomicFeatures version at creation time: 1.50.2
RSQLite version at creation time: 2.2.19...NA
Nb of transcripts: 40735
Db created by: GenomicFeatures package from Bioconductor
Creation time: 2022-12-06 16:31:04 -0600 (Tue, 06 Dec 2022)
GenomicFeatures v…
updated 3.1 years ago • oluwamosope
save(labels, file = "sampledModuleExample-matchedLabels.RData")
sessionInfo( )
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu...Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line…
updated 3.5 years ago • as8020
the same sample and ranked them from the most expressed to the least expressed. I cannot use counts nor normalized counts because they do not take into account the gene lengths. Which measure would you suggest I use? Does DESeq2
updated 7.0 years ago • chiara.facciotto
<div class="preformatted">(1) Anova for 12 Affy yeast chips (Yg98)
I'm going to try to explain the problem in a better way. I have the
following experimental design :
Fraction 1
Fraction 2 Medium A
Fraction 3 * Medium B * 2 Reps
- Fractions 1, 2 and 3 are three distinct subcellular mRNA populations
;
- Medium A and B are two distinct culture m…
condition)
dds <- DESeq(dds)
res <- results(dds)
# Use lfcShrink to generate more accurate log fold change towards zero by shrinking lfc
resultsNames(dds)
resLFC <- lfcShrink(dds, coef=2)
#print all data
res_alldata...as.data.frame(resLFC), as.data.frame(RPMmatrix), by="row.names")
sessionInfo( )
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Runnin…
updated 2.3 years ago • Shihui
CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to
re-install: 'clusterProfiler...CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Warning message:
package(s) not installed when versio…
updated 3.2 years ago • xqhuqd
Hi, I am a very new R user, attempting to install bioconductor packages on my mac (R version 4.2.1, macOS 12.4 Monterey).
With attempted installation of bioconductor packages using either v3.15 or 3.16, I run into the following:
```> library(BiocManager)
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
> library(BiocVersion)
> library(BiocParalle…
updated 3.5 years ago • mvictor
following commands, I get M and A values.
write.table(MA.p$A,file="h:\\r\\Exp200\\single channel nor A.txt",
append
= FALSE, sep = "\t", eol="\n", na="NA", dec="")
write.table(MA.p$M,file="h:\\r\\Exp200\\single channel nor M.txt",
append
= FALSE, sep = "\t", eol
updated 21.5 years ago • Binita Dutta
div class="preformatted">hi to BioC list,
I have one question
about gcRMA: if I
run
nor<-gcRMA(affy.data)
after the background
correction, then
what methods does it
use? to me it's not
clear if it use the
usual
updated 20.5 years ago • claudio.is@libero.it
is not available (for R version 3.2.0)_
Neither of I use install.packages("GenomicFeatures"), nor with biocLite("GenomicFeatures"). And therefore, I can't load the package to do my analyses.
Does anyone have any suggestions
updated 10.6 years ago • jcotignola
Hello,
I'd like to run edgeR on a MeDIP-Seq experiment with 4 treatment groups (each with 5 samples). I'm counting reads in slides over the genome (a few hundred bases with some overlap).
I realised that there is a small batch effect as both IP and input separates per treatment group in an MDS plot (limma::plotMDS) of the count matrix. I can't simply add a batch factor to my model as this is co…
updated 10.2 years ago • Arne Muller
CRAN: https://cran.usk.ac.id
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Installing package(s) 'ggtree'
trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/windows/contrib/4.2...still like that >:(((
# https://support.bioconductor.org/p/9139604/
My latest R version is 4.2.1 (2022-06-23
updated 3.3 years ago • Muhammad Isa
Recent ...
Replies
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
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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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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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?
by
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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80
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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