validity
df <- DataFrame(matrix(ncol=3, nrow=2), check.names=FALSE)
# assign names which would be changed if "check.names=TRUE"
names(df) <- c(1:3)
# names are as specified:
df
#DataFrame with 2 rows and 3 columns
# 1 2 3
# <logical> <logical...NA
#2 2 NA NA
# assign using '[['
df[[2]] <- 3:4
# colnames are now changed…
Order by: Relevance
3 |
My goal here is to descriptively show how gene expression for certain genes of interest changes across the samples, by describing fold-changes or by plotting normalised units of gene expression. I am interested...in eyeballing relative change without formal differential expression analysis as there are no replicates here.
I would like to use the GeTMM method
updated 5.9 years ago • rachael.lappan
other than
fold change (section 5 of the tutorial). And you may always compare
the effect of using different per gene scores/statistics as in...section
5.
It is not likely to generate false positive no matter you use fold
change or other test statistics in GAGE analysis given that GAGE test
the mean of tens or hundreds of genes in a gene set or...false positives.
On 8/28/2014, Chun wrote:>…
question/concern about P value calculations in Limma (I
am
using latest version of Bioconductor)
I recently ran 3 arrays through my analysis. The slides were
analayzed
with Genepix software. There were a couple of genes that...concerned
me.
One had a log fold change of -3.765. The adjusted p-value (fdr)
was .027. I looked at the individual M values for the arrays and they
were -0.009336, 0.0…
useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="www.ensembl.org") # reflects recent change to hosting, as discussed in https://support.bioconductor.org/p/74322/
genemap <- getBM( attributes = c("ensembl_gene_id
__ID "ENSMUSG..."__ rather than the typical __gene\_id "ENSMUSG..."__. I realize that I can change these pretty easily afterwards with a script, but I was wondering if there is a way to modify the export behavior? Thanks
updated 10.5 years ago • Jake
rows and 10 columns
[5] sa: SummarizedExperiment with 20 rows and 10 columns </pre>
And i want change "sa" in "exp\_3".
Thank you
updated 7.3 years ago • mario.zanfardino
way to do this?
My naive thought was to just multiply the original count data by whatever fold change factor before it goes into the Splatter parameter estimation, but I'm sure this is suboptimal if not just simply inaccurate
updated 7.2 years ago • Brian Haas
of text here
Hi, there:
I read the previous posts about deriving confidence interval for fold change using DESeq result at URLs: https://support.bioconductor.org/p/9142141/ and https://support.bioconductor.org/p/80725...80729
one comment from Micheal Love mentioned:
Estimated standard errors for the estimated coefficients on the log2 scale are given...by the lfcSE column. Yes, you can c…
updated 3.3 years ago • Mike
fgem available="true" name="E-GEOD-28146.processed.1.zip"></fgem>
>
> Perhaps ArrayExpress changed "count" to "available" (it still says
count="true" for raw data files). In any case, changing queryAE from
fgem[@count] to fgem...the issue.
>
>
> But as you're probably aware, the XML file from ArrayExpress
includes this comment:
> This section is …
updated 12.8 years ago • Ibrahim Emam
<div class="preformatted">Hello,
I am hoping someone will be able to help me with this. I am analyzing
the two color common reference design agilent arrays using Limma. I
have four replicates and two treatments(control and PCB). I am trying
to extract fold change values (PCB/control) for the four replicates
separately. lmfit() command after normalizing between arrays is
pooling all the sam…
Fold to be log2(treatment - control)
My issue is that I find the results to be inconsistent when I change the settings of the contrast, and I don't know which method is valid.
First approach is the automatic way:
```r
DBdata$contrasts...NULL
DBdata <- dba.contrast(DBdata, categories = DBA_CONDITION)
DBdata <- dba.analyze(DBdata, method=DBA_ALL_METHODS, bParallel = TRUE)
d…
Hello, I would like to know if using the cnetplot function, I can choose a specific category to graph. For example, if I have three categories, graph each one independently
updated 6.4 years ago • MperezM
I've used BiomaRt to map Ensemble to Entrez Id's and Uniprot Accession Id's . Recently, biomart made some changes and it seems that Unimart is no longer available? If i try this code (that was working before...mismatch: body line 4 and html
6: Premature end of data in tag html line 2</pre>
I tried changing the host option as I did with the Ensemble :
<pre>
listMarts(ho…
from the webserver as well as running it locally, it seems that the format of PFAM result files has changed and they are no longer compatible with ISA. I also wasn't able to reformat them because there are a few columns missing
updated 5 weeks ago • bolusharris
<div class="preformatted">Dear All,
I would appreciate it if you would let me know how to change the scale
of
my data tracks when plotting on Gviz. My data ranges from 0-0.4 in
values
but I want to keep the scale as 0-1 for...div class="preformatted">Dear All,
I would appreciate it if you would let me know how to change the scale
of
my data tracks when plotting on Gviz. My data ranges …
How may I change the row names of an assay to make it more compatible with other R analysis?
```
> class(cancerAssays)
[1] "MultiAssayExperiment
updated 5.2 years ago • Dario Strbenac
some of the three replicates of one gene are all 0 reads count, why it still can be count log 2 fold change, or I misunderstood something
updated 3.8 years ago • YATING
in a t-SNE plot. I am using Scater and Scran packages for scRNA-Seq data analysis. I also want to change the color palette but could not achieve it too.
I used +geom_label_repel(data$clusters) but R crashed with that command
I am not able to find the R command to obtain the list of Differentially expressed genes at a Fold change (log-fold change) and FDR cut-off. The R command __summary__:
<pre>
summary(de <- decideTestsDGE(et, p=0.05, adjust="BH"))</pre>
only...top "n" number of DE genes.
I am interested in getting the__ full list of DE genes at the log fold change cut-off of (+-1) and FDR cut…
div class="preformatted">Dear all,
I recently encountered an unexpected behavior of the GenomicRanges
flank function.
When using it with ignore.strand=TRUE...of length 1
start end width
[1] 2001 2100 100
Is this behavior intended? Any help or comments would be much
appreciated.
Leonard
--
Leonard Goldstein, PhD
Postdoctoral Research Fellow
Department of Bioinformatics
updated 12.6 years ago • Leonard Goldstein
Hi,
I've got a simple A vs B model design in Limma for 450K data (M-Values to avoid Heteroscedasticity), but I'm struggling with figuring out a fold change cutoff in topTable. If I had beta values, I could simply set a cutoff of 0.1 to see things with at least a 10% difference in...for 450K data (M-Values to avoid Heteroscedasticity), but I'm struggling with figuring out a fold change …
that is DiffBind (at least by default) not using DESeq2's MLE estimation when calculating (log) fold change. So the concentration of DiffBind equals precisely log2(mean across condition), while the DESeq2 log fold change does...0.0000000 0.0000000
ZR751 ZR752
25.0813852 10.9513965
```
DiffBind fold change = Conc_MCF7-Conc_BT474
ConcBT474 is precisely log2(mean(BT4741,BT4…
updated 4.7 years ago • Sam
had any problems with the annotation or codelink data once
exported from the Codelink App, i.e. changing accession IDs.
I apologise in advance for not having the codelink version number to
hand but can't access my laptop
updated 16.5 years ago • Matthew Neville
I have recently got an email about the package that we maintain. I fixed the issue and committed to the repository, however, I get the...XXXXX/malbec2-checksrc.html
Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org
<div> </div>
 
updated 7.4 years ago • hamedhm
was unable to read the image processing files listed
in the targets file". I have this problem with recent data, but with
previous data the package worked. Why?I have changed nothing in the
procedure (analysis of images and exporting
div class="preformatted">Hello,
I recently upgraded to rw1071, copied old packages to new library,
used
pull-down menu's update command for Bioconductor. Got...cannot open: HTTP status was `404 Not Found'
In addition: Warning message:
DLL attempted to change FPU control word from 8001f to 9001f
[[alternative HTML version deleted]]</div
updated 22.5 years ago • TyagiAnupam@aol.com
div class="preformatted">Hi,
I recently updated R v2.3 and BioConductor 1.8. I tried to use
justGCRMA,
but it's giving me the following error. My code has always...worked in
the
past. Can someone help point out my error?
Thank you,
Edmund Chang
> pd <- read.phenoData("pheno.txt", header=TRUE, row.names=1)
> eset <-justGCRMA(filenames= rownames (pData(pd)), phen…
updated 19.7 years ago • echang4@life.uiuc.edu
comparison of one condition against groups of other conditions.
I think that this has to do with a change in the version of DESeq2 and someone updated the lab computer. Unfortunately I had not saved the sessionInfo() previously
updated 9.6 years ago • Ira
by arrayWeights are implemented
to the the lmFit function how are calculated the log2 fold change
(coefficients ) ?
I tried to calculate them by myself applying the weights to the
samples but I couldn't get the same results
I want to calculate disease semantik similarity. Bu I couldnt run the this code in category "C".
hsamd <- meshdata("MeSH.Hsa.eg.db", category='C', computeIC=T, database="gendoo")
Please help me
updated 6.7 years ago • ahmettoprak42
that I was given.
The data is formatted in the below format. Note that I've acquired the fold change data as the peaks for each sample are quantified as either a 0 or 1 rather than a range in between. Therefore, I don't think...it would be as useful for normalization as the fold change values themselves.
I've tried doing successful calls to dba.peakset for each sample to generate a new DBA …
updated 2.8 years ago • ssankar3
div class="preformatted">
Hello Jordi,
My comments to your questions are below. I hope this helps. -Denise
______________________________________________________________________...x,lambda,p=0.1) [[1]]
>mainDIgenes<-sapply(lm.f.Fsub, FUN=mainES)
#####
# See above comments.
#####
## To get the genes characteristics of the diabetes+treatment:
>for (i in 1:length(lm.f))…
updated 21.7 years ago • Denise Scholtens
Everything works well, but in the output of the topgenes() function i
do not understand how the fold change is processed.
Has anyone a hint?
It is not just the difference of the mean like in limma. Even in the
papers of breitling
div class="preformatted">Changes to the annotate package is expected to take place in two weeks
that will
involve removing all the data files for Affymetrix
updated 23.5 years ago • John Zhang
Hello,
I have some questions about releveling to reset the factor level.
I am running an experiment in DESeq2 with 4 stages that I want to compare to each other under one treatment. My goal is to change which factor is the reference for generating result outputs. I understand that the default is the 1st factor, by...in DESeq2 with 4 stages that I want to compare to each other under one…
updated 9.8 years ago • rclaire
a color label?
2/ Any way I can make my modules labeled with more "normal" colors? Or any way I can change the module colors manually?
Many thanks!
YS
Part of the code:
<pre>
dynamicMods = cutreeDynamic(dendro= geneTree, distM
updated 7.2 years ago • dcxy18
available on [http://m.ensembl.org](http://m.ensembl.org/).
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\_82 <- useEnsembl...Gene ID" filter for the miRNA Target Regions dataset
A complete list of the changes in release 82 can be found at&am…
I have expression data for a pure MEF sample grown under similar conditions.
I'd like to do a fold change analysis between time points, subtracting the MEF expression contamination in such a way that the resulting increased...variance per gene is factored into the fold change analysis.
It seems it may be possible to do it within DESeq2 or using svaseq but I can't figure out how. Can anyone reco…
to do a PCA plot with the package affycoretools, which I
have
found very useful!
I am not able to change the situation of the legend in the plot,
although I
have introduced the variables x.coord and y.coord in the script...utils" "datasets" "base"
other attached packages:
rat2302cdf affycoretools GOstats Category hgu95av2
"1.12.0" "1.4.0" "1.6.0" "1…
TRUE,
trace="none", cexRow=0.8, cexCol=1.1, margins=c(8,32),
main=paste(name,
'_', dim(tabNew)[1], ' categories', sep='') )
I work with R.2.6 version.
How can I achieve this? I do not want to change my values and make
them
symmetric, as I
for my experiment. We looked at
three age groups of rats (YA, MA and OA) to look at gene expression
changes following LTP (LTP is a memory model). LTP was stimulated on
one side of the brain, while the opposite side served as control...How can I differentiate the groups in a model matrix? I would like to
compare the gene expression changes between the three groups. I would
have liked to look at t…
updated 4.9 years ago • Carthika Luxmanan
I am having trouble determining what values I need to use for determining “significant differentially expressed genes”
I have been asked to attempt this using two methods.
Method 1 involves the use of the pipeline used in our lab which involves mapping to HISAT2 -> normalizing with cuffnorm -> getting FPKM values -> getting the LOG2FC of those and performing a T.Test for P …
updated 7.2 years ago • Harrisonesmith
with minOverlap=1 (all peaks to be included in the consensus peakset). However, dba.blacklist changes the consensus peakset to be based on minOverlap=2. How to run dba.blacklist without changing minOverlap?
```r
dbObj_blacklist
updated 2.1 years ago • Sam
Hello
I have some protein *.msf file. I can not open it.
Which software or R package that can change this kind of *.msf to any readable file?
Thanks in advance for great help!
Best,
Yue
updated 5.1 years ago • yueli7
If choosing EDGER for my dab object should I choose one of the TMM normalized score categories in dba.count?
Trying to figure out which of the these categories makes most sense for my ATAC-seq data.
Thanks
updated 8.9 years ago • rbronste
<div class="preformatted">Hi there!
I've run into a problem with biomaRt and the biomart on ensembl.org.
When I try to load the Ensembl Genes 67 I run into trouble. Until a
month a go it did load like it should. The strange thing is when I use
the same code but change the host from "may2012.archive.ensembl.org"
to "www.ensembl.org" it loads without any trouble. Other archived
hosts also …
to adjust the range of the x-axis,
which I believe is somehow set to a fixed 150 bp. If I was to change
that to 100 bp for example, how would that work?
Thank you very much for your help!
Best,
Tobias
--
Tobias Hohenauer, PhD
GCNA
was upgrading to the newest R version, but I'm already running R 3.1.1. I do realise that I need to change the contributing url. However I do manage to do that? the argument is embedded deep into the biocInstaller and I do not
updated 10.1 years ago • ail27
by
checking the M values)...
Could someone please clarify how do i correctly interpret this fold
change as it is not straight forward for me to extract this
information from the matrix.
Thanks in advance,
Christian
--
The University
div class="preformatted">Hi Jingqin,
Thanks for the comments and interest!
We do provide some decent utilities in the gage package for Result
Presentation and Intepretation...vignette for details.
I used GSEA quite a while ago. I am not that familiar with the output
from its recent versions. If you want some html/webpage type of
output, gage package don?t do that at this time. But we may consi…
updated 15.1 years ago • Luo Weijun
I have recently obtained very promising results using the diffSplice and diffsSpliceDGE from limma/edgeR, respectively. I was...using the Simes method different from using DEXSeq perGeneQvalue? Does it possibly relate to the comment that "The exon-level tests are not recommended for formal error rate control." from the help files?
Any insight or pointers
updated 9.4 years ago • maltethodberg
2.10 and R 2.15
in
> the instance).
>
> I've been able to run RStudio. ?However, I can't change into a
> different directory, e.g. setwd('/root'), that is accessible when
you
> login via ssh. ?Motivation is that I would...a different directory or on a different mounted EBS volume.
> Is this a situation where I need to change some of the permissions?
&…
Hi Aaron,
In the code of `scran::pairwiseTTests` (current version on Github), you have this commented out:
> In theory, a better weighting scheme would be to use the estimated standard error of the log-fold change to...single gene, two blocks, and two groups. The sample size is equal across blocks and groups. The fold change is the same in the two blocks, but the first block has more zer…
updated 4.1 years ago • Angelos Armen
untreated data. I have used DESeq2, using `` normTransform(), ``to calculate the pairwise fold-changes. So Initially I have 60 samples and now I have a Fold change matrix of 30 columns and for all genes.
<pre>
GeneID sample1_T...which represents the number of samples the gene shown to be up/down regulated and extent of fold change, such that I can use that score to …
updated 9.8 years ago • g.atla
div class="preformatted">Colleagues,
The functioning of the DAVIDQuery package was disrupted by
a recent change in the formatting of web pages that we parse.
(Yes I know, but there's no real API.) There are also more stringent
http
updated 15.6 years ago • Day, Roger S
extremely
dynamic
area etc., I'm somewhat worried whether this is actually possible.
Does this
much change in less than a year sound realistic to list members, or
should I
start bug hunting?
Thank you!
alexander
Alexander.Ploner
updated 22.8 years ago • Alexander Ploner
like to find all genes that show less than a 2fold increase in condition A vs B, wether the fold change is positive or negative. (and reciprocally genes that show not a 2fold decrease). Is that possible?
I tried results
updated 10.8 years ago • samuel collombet
growth over 4 biological replicates per each condition.
A collaborator constructed a graph of fold change from that output for approximately 15 genes of interest.
I have a request from a peer reviewer to provide error bars
updated 9.7 years ago • lisa.crossman
count data, and I generate my dds object from phyloseq.
_dds = phyloseq\_to\_deseq2(mouth, ~ category)_
I am interested in performing tests of how OTUs/species in different oral diseases within the mouth differ...5 different disease states including normal.
I have defined "normal" as the reference category as follows:
_dds$category <- relevel(dds$categ…
updated 8.7 years ago • negic4
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