We recently commissioned some RNASeq work and I am getting my first taste of using bioconductor. This is probably a bit of a silly...a reasonable design?
3. When comparing results between cell lines, I assume I need to compare fold-changes. Are there methods in bioconductor that can compare two DESeqResults objects?
Any feedback, pointers, or advice greatly
Order by: Relevance
s Memorial Hospital
in Chicago. I'm using the edgeR library to compare RNA-seq datasets.
But, recently I was running a comparison and got an error that led me
to the realization that some of the p-values were being returned...as
"NaN". I searched the message archives and found messages addressing
the Fold Change sometimes showing up as NaN but this is the p-values
in my case. I checked the inp…
<div class="preformatted">Hopefully I can get a quick answer to this question about GOstats.
I'm trying to calculate enrichment for every GO category using the
GOstats
package. I would assume that setting the p-value cutoff = 1 with
conditional=FALSE would give me an enrichment odds ratio/p-value for
every
GO category in, say, the BP ontology. However, this does not seem to
be the
case, as…
updated 13.7 years ago • Andrew Jaffe
654, 611
3378, 3080, 2190, 1491, 1001, 1470, 1199, 1288, 874, 794, 515, 783
The genes in both categories have comparable baseMean expression.
Why should not the genes in the first group also be considered as outliers...Under specific circumstances, is it correct to change the cutoff of what is considered a dispersion outlier?
Is there a parameter that controls it?
Thanks you very much …
updated 2.7 years ago • raya.fai
weird results with two genes on the Y chromosome having significant LFC between males (reference category) and females (comparison category), which is little bit unexpected from my taste. Indeed, I am expecting to have only
updated 2.1 years ago • Loïc
Hello,
This is the first time I use Limma for multiple (three) categories comparison. From the tutorial, I use make contrast to compare every two categories. Let's say A,B,C.
contrast.matrix
updated 10.1 years ago • bharata1803
is exactly what the log-ratio
analysis would tell you.
On the other hand, if you average the fold changes, you get nonsense
results. The two fold changes are:
10 and 1/10
so the "average fold change is a bit over 5. So you conclude...is 10 fold down in the
unstimulated condition and the second is 10 fold up. So the two fold
change
are:
1/10 and 10
so the "average" fold change is again a bit …
<div class="preformatted">
Hello everyone,
I would like to ask for your help and appreciate any comment from you!
Here is my question:
I want to compare group A with group B using a reference design by
cDNA arrays and find DE...<div class="preformatted">
Hello everyone,
I would like to ask for your help and appreciate any comment from you!
Here is my question:
I want to compare …
Hi, I am new in R and I have performed DESEQ2 analysis and I am confused at a particular step
I try to plot the normalized counts into box plot but it does not match with the fold change results generated by Deseq2
For instance, using CADM2 gene as an example and I compared OAC wBE with normal mucosa. The...step
I try to plot the normalized counts into box plot but it does not match with the …
updated 4.6 years ago • Chloe
for affy cdf kindly provided by Ariel Chernomoretz.
The function was failing with the error
cannot change value of locked binding for 'hgu133plus2probe'
I found that adding the line
unlockBinding(probepackagename,as.environment
Dear community,
After creating an expression set for the PorGene-1\_1-st affymetrix array. I found out that many of probes do not have annotations. As a result, once I am done with differential expression analysis, I found out many regulated probes that do not have any feature assigned assigned. These is highly problematic to do pathway analysis.
I got the annotations by using the func…
updated 9.9 years ago • serpalma.v
```{r}
#make a gene network from enriched pathways
options(ggrepel.max.overlaps = Inf)
## convert gene ID to Symbol
edox <- setReadable(gse, 'org.Mm.eg.db', 'ENSEMBL')
p2 <- cnetplot(edox, categorySize="pvalue", showCategory=16, foldChange=gene_list, node_label="category")
```
I'm using the above code to try to make a gene network for some pathways enriched in my GSEA data …
updated 23 months ago • Grace.Ciabattoni
the code I am using to make the heatmap (this is the same for both heat-maps, only stringasfactor changes).
Ben
<a href="https://ibb.co/Tw69Stc"><img alt="stringasfactor-F" border="0" src="https://i.ibb.co/sgn8Gqj/stringasfactor-F.png
I recently performed RNA-seq analysis on auditory brainstem of mouse.The experiment involves wildtype mouse brains vs...I recently performed RNA-seq analysis on auditory brainstem of mouse.The experiment involves wildtype mouse brains vs a transgenic mouse where two microRNA,s are knocked out. The idea was to see the difference in expression of genes between wildtype vs KO as microRNAs regulate g…
updated 3.2 years ago • faiza
div class="preformatted">I'm seeing a noticeable performance change in goTools' ontoCompare()
from BioConductor version 2.3 to 2.4. With the same input data the
user time reported by system.time
updated 16.6 years ago • Scott Markel
sure that I did the exact same thing but the versions of the DESeq2 packages.
I'm wondering what's changed in the algorithm.
I appreciate your help in advance
updated 8.2 years ago • Yang_Zheng_Neuro
preformatted">Dear all,
The new Ensembl marts for release 71 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...from the interface for this release. They will be
reinstated in release 72.
A complete list of the changes in release 71 can be found at
http://www.ensembl.org/i…
to announce that the new Ensembl marts for release 76
are now 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...Added "QTL chromosome name" and "QTL region" filters for sheep
and chicken
A complete list of the changes in release 76 can be found at
http://www.ensembl.org/info/web…
updated 11.4 years ago • Thomas Maurel
calls, like chr2.161597652 (millions of
them), and would like to classify them into the following categories:
1) exon, 2) intron, 3) UTR, 4) intergenic. For the first 3 categories,
it would be great if the gene name could also be identified
<div class="preformatted">Hi Matt:
I should have replied to this earlier, but I'm monitoring the list in
digest mode... My comments below are to Matt, but referring to
Robert's
last reply.
> If they have no probes in common, and were applied to the same RNA
> (essentially technical and not biological replicates) then the two
> arrays can be combined into essentially …
updated 20.3 years ago • David Henderson
<div class="preformatted">Dear all,
Recently we have performed a microarray time-scale experiment
including
different time-points (0h, 2h, 6h,
). Treated and untreated cells were
compared by competitive hybridizations for every time-point using
dual-channel microarrays. Every time-point was performed in triplicate
including 3 biological replicates.
Microarray analysis is performed in R wi…
updated 18.3 years ago • Serge Eifes
Hi!
I am observing different statistics for DE analysis done in two separate runs executed on same count files. Apart from base mean, all other columns have different statistical numbers for every row.
Perplexing thing is that normalized counts are same for both the runs but pValues and log fold change values are still different. The only thing done differently from the earlier run is that …
updated 23 months ago • Kuldeep
specific pvalueCutoff...
```
I got nothing. Therefore, I also tried org.Mn.eg.db, because I recently performed a similar analysis on mouse datasets and got a result with more than 1000 categories.
```
> HuSplCD103nEqCD103pEq_GSEA...done...
There were 23 warnings (use warnings() to see them)
```
The result contained 817 categories.
What caused this difference? Is simply GSEA i…
updated 19 months ago • sawa
identifies 6 differentially expressed genes, with almost every gene having the incorrect log2-fold change difference between the groups. In contrast, the log2-fold changes calculated between SCFM2 and AZT/BHI are correct...p-value cutoff of 0.05)
#You can specify the specific growth conditions for pairwise comparisons by changing the name of the conditions to compare
resLFC_TOB <- lfcShr…
updated 4.6 years ago • Naphtap92
<div class="preformatted">Dear Biocore Team (and users of GOstats):
It appears that the Sanger URL format has changed for the Pfam site,
which causes broken links when using summary() with option
htmlLinks=TRUE. Below is a comparison of...preformatted">Dear Biocore Team (and users of GOstats):
It appears that the Sanger URL format has changed for the Pfam site,
which causes broken link…
<div class="preformatted">Hello, All!
First I'd like to thank all people who are working on
Bioconductor project - you are doing great job!
I'm new to this list, to R, to all that biocondactor things, and
actually to the statistics it self... so please
excuse me if I'll ask smith trivial.
I'm doing the clusterization of the microarray data. Here is the
example of my routine
sample.files&…
updated 21.4 years ago • tiv_
if anybody could give me pointers on how to use
GOstats with
a custom list of gene annotations/categories
I have my list of yeast genes associated with one or more of 25
different
categories
My file looks something like
updated 16.9 years ago • Iain Wallace
Hi!
I hope you’re doing well during this strange and chaotic time.
I conducted WGCNA for my RNAseq data with 18000 genes, and got some nice modules that seemed to have very good eigengene values with the traits I’m interested in. Then I tried to look for hub genes in these modules and also try to visualize the networks. However, since most of my modules of interest are a little big, contain…
updated 5.8 years ago • minyaaa9058
Dear All
Any help with this would be appreciated. I am normalizing a number of
U13A
affy chips with justRMA and upon comparison of the pre- and
postnormalization histogram curves, I see what seem to be some
anomalies in
the post-normalization ones. The post-normalization curves that I have
seen
from other people most often look much smoother than what I get. I
attach
two graphs for you to inspec…
sort by subject. I
sent one email to myself with the subject "test1" and then replied to
it
without changing the subject. The reply correctly went to "test1" in
the
inbox sorter. I then changed the subject heading in the test1...you started
writing the message as a reply to something completely unrelated,
specifically: "Re: [R] change plotting symbol for groups in trellis
graph". You should not d…
updated 19.0 years ago • Kimpel, Mark W
reply from server.
My intention was to analyze the data using lfc = log2(1.25), since this fold change give interesting results using the enrichPathway() function of the ReactomePA package.
Many thanks for any help and
updated 8.0 years ago • jan.soderman
information you give.
You say that you did an analysis a few months back, and another
analysis
more recently, and got somewhat different lists of genes. But you
don't
tell us what the two analyses were or how they were different...that
at least one of them is a single channel approach. It's not much to
go
on! There has been no change to the limma code in the meantime, so it
much be your analy…
new Ensembl marts for release 88 are now live on www.ensembl.org.
If you are using biomaRt, you can change your host to access our most recent data:
<pre>
ensembl_mart_88 <- useEnsembl(biomart=“ensembl")</pre>
Change affecting...nbsp; Region filter performance improvement
Vega 68
You can find the complete list of the changes at http://www.ensembl.org/info/webs…
updated 8.8 years ago • Thomas Maurel
27128 3.870369
The outcome looks fine, with genes with p-values below 0.05,
independent
of fold-change (and genes have been confirmed in 'Resolver').
However, I want separate files for probe sets with logFC>0
(upregulated...lt;0 (downregulated), but the option lfc=0 does not
distinguish
between positive or negative fold change. I have tried lfc>0 and <0,
but the function…
updated 17.4 years ago • Wijchers, Patrick
The legend text is too small and the colors I would like to invert to have the mutant in red... or change it to blue.
I would like to make the output plots better to include in a publication
out.groups <- see.genes(get.groups
Hi,
I recently installed the org.Mm.eg.db package and for about a week I was able to load and access it perfectly. However, now when...Hi,
I recently installed the org.Mm.eg.db package and for about a week I was able to load and access it perfectly. However, now when I try load the package I get the following error:
library('org.Mm.eg.db')
Error: package or namespace load failed for ‘o…
updated 4.7 years ago • Jack
and it still runs correctly for
me,
using either R 2.15.1 or R-devel on Windows.
There weren't any changes to that part of the limma code between R
2.14.1
and R 2.15.1, so the change you are seeing may be in the stats
package.
Best...type fault
(windows)
Marcus Davy mdavy86 at gmail.com
Tue Sep 4 07:11:43 CEST 2012
Is anyone having recent problems after upgrading to R-2.15.1 on
windows
with li…
updated 13.4 years ago • Gordon Smyth
I used the following code to account for batch effect:
db.counts <- dba.contrast(db.counts,
categories=DBA_CONDITION,
block = DBA_REPLICATE, # block design
minMember = 2)
db.counts <- dba.analyze(db.counts)
db.results...all the output csv files are the same as above.…
updated 6.2 years ago • liruiradiant
I have a very specific question regarding the dotplot function from enrichplot:
Example data from [enrichplot tutorial][1]
library(DOSE)
library(enrichplot)
data(geneList)
de <- names(geneList)[abs(geneList) > 2]
edo <- enrichDGN(de)
edo2 <- gseDO(geneList)
dotplot(edo, showCategory=30) + ggtitle("dotplot for ORA")
dotp…
updated 2.6 years ago • Tyroone
Dear all,
Changes to Ensembl data access and APIs are coming as we transition to our new platform.
This includes updated services, archive
0.5mM and 1.0mM of a drug with which cell
cultures get treated. The 0.1mM dose causes hardly any change in gene
expression, whereas there's a big difference in gene expression at
0.25mM.
Then at 0.5mM and 1.0mM the reponse...scenario.
The problem is that many genes within one experiment behave like
described
above, otheres change linear others exponetial ...
Could I still use lm for this kind o…
diffobject.3,design=T)
# No-design approach (pre-3.00)
diffobject.2 <- dba.contrast(diffobject,categories="Condition",group1=dba.mask(diffobject,"Condition","TREAT"),
group2=dba.mask(diffobject,"Condition","CONTROL"),name1...2. Different p-values for the same regions, probably related to the above
3. Differences in fold change: In the no-design approach I obtain fold changes that ar…
updated 4.4 years ago • Roger
Sir,
>
>
> Thank you for helps.Again iam facing some problems in raedCtData
> step. i changed exFiles$File[c(1:30) it reads 30 sample but when i
> change to exFiles$File[c(1:99) then it is showing error. could you
> tell...lt;- factor(c("Marker", "TF", "Kinase") in my
> case it is cyclins and cyclin inhibitors where to change that.
>
You can…
on two different conditions). As part of the analysis
I'm doing a GO analysis. There are a few GO categories of special
interest, so I want to extract data for the probes identified in these
categories and cluster the data...seem to match that
from "geneIdsByCategory." Specifically, the number of unique EntrezIDs
in each GO category are different. Here is some example output (only
showing results…
updated 12.9 years ago • Guest User
sample that is assigned to each functional category. There
are a number of ways to bin the samples into categories, based on some
other analysis I'm most interested in a...breakdown into two subjects
and 5 temporal categories within each subject, i.e. a total of 10
categories. Two of the categories have 4 samples each, the remaining
8 categories...would expect the permutations to be
fairly nois…
updated 14.6 years ago • Les Dethlefsen
sample that is assigned to each functional category. There
are a number of ways to bin the samples into categories, based on some
other analysis I'm most interested in a...breakdown into two subjects
and 5 temporal categories within each subject, i.e. a total of 10
categories. Two of the categories have 4 samples each, the remaining
8 categories...I definitely want, since I don't
think the dist…
updated 14.6 years ago • Les Dethlefsen
has both mutated and wild type representation.
3.The number of wild type is more within each category than the mutated thus cancer_subtype1 can have 3 samples with wild type genotype and only 1 of that mutated.
4.**Number...12] "geneX_mutationwildtype.cancer_subtype6"
*So, first I am losing the geneX_mutationmutant category comparison. I am also seeing only a few comparisons betwe…
<div class="preformatted">
I have question arising to the pooling of mRNA
samples. Someone approached me about the
following problem:
The study wants to use Affymetrix chips to study
changes in expression between a group of treated
mice and a group untreated mice. There are 10 mice
in each group. It is only possible...Someone approached me about the
following problem:
The study wants to u…
updated 22.3 years ago • Wiesner Vos
I am looking for the exact formula for the calculation of Fold Change (FC), p-val and q-val in Ballgown stattest?
By using gexpr I got the gene expression values for the list of genes. For better
updated 7.8 years ago • ag1805x
Dear list,
I am a fairly new user of R and I am currently trying to use the HTqPCR package to analyze qPCR data derived from the Biomark platform (96.96). For each chip I have 9216 Ct values, of which I wanted to eliminate those below or above a certain threshold. I tried to use the setCategory and filterCategory function for this purpose but ran into problems (I did not get any warning messag…
updated 6.0 years ago • saskia.trump
Hi,
The following code used to work in R 3.3 with Bioconductor 3.4. It now fails on a linux machine I have access to with both Bioc 3.5 and 3.6 but works in my OSX laptop with the same versions.
library(bumphunter)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
gene <- annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg38.knownGene,
annotationPackage = 'org.Hs.eg.db…
updated 8.3 years ago • Leonardo Collado Torres
I have been trying to change font sizes for my box plots in DiffBind:
<pre>
dba.plotBox(x, th = 0.05, pars = list(cex.axis=1.5, cex.main=2, cex.lab=1.5))</pre...I have been trying to change font sizes for my box plots in DiffBind:
<pre>
dba.plotBox(x, th = 0.05, pars = list(cex.axis=1.5, cex.main=2, cex.lab=1.5))</pre>
I
updated 7.6 years ago • Mthabisi Moyo
<div class="preformatted">Hello Gentlepeople,
I have been using the edgeR package to identify differentially
abundant
tags in an RNA-seq experiment.
I was happy when the edgeR package version 2.4.6 called 41
differentially
abundant tags.
However, now I am unhappy because the same analysis with edgeR package
version 3.0.2 does not call any differentially abundant tags.
I've compared the …
for more details.
II What is new?
o Third release based on Knoppix 3.4 with many changes from both
new and
updated packages, still based on Knoppix 3.4 and the
clusterKnoppix
release from May 10 with kernel...complete debian-med of everything but the cms
package
(would Zope make sense for Quantian -- comments welcome!)
- the GNU geda program suite for electronics …
I was asked to run DESeq2 on RNA-seq libraries, 2 replicas x 2 conditions (I know it is not ideal but that's how the data is). I notice that there is a small subset of about 20 genes which only showed up in one replica of one condition (and I think this is due to contamination in the second replica):
raw reads:
cond1.1 cond1.2 cond2.1 cond2.2
geneA 0 0 0 1376
…
updated 5.7 years ago • ninova
hello,
there is a minor problem with links in the hierarchy of tasks at bioc
views [1]. the top category is subdivided into software, annotation
data, and experiment data. clicking on software/biological domains
leads...to a task view where the are no packages, and the parent
category
is experiment data rather than software.
vQ
[1] http://www.bioconductor.org/packages/release/BiocViews.html
…
method but not
if you
use the approximation. It's not clear to me why it's not working for
the
down category but does the pwf look ok when you generate it? Are there
many
genes DE for the down list?
Cheers,
Alicia
> Message: 1
>...gene2cat=hs.go,
> test.cats=c("GO:CC", "GO:BP", "GO:MF"))
> Using manually entered categories.
> Calculating the p-values...
>…
question has popped up over and over again in this forum. The simple solution is to remove redundant categories to make rank full again. I would like to go further than this simple approach and figure out a conceptually more...tbody>
</table>
Apparently, the design is faulty ("not full rank"), because the "Strain" category has been accounted for by the "Virulence". In other …
Hello there,
My issue is that DESeq no longer works and does not give me the correct contrast options. This was working before I updated to DESeq2 1.22.2
Here is my code:
```
> line.ds <- phyloseq_to_deseq2(ps.phyla, ~ Line)
> diagdds <- DESeq(line.ds, test="Wald", fitType="parametric")
using pre-existing size factors
estimating dispersions
found already…
updated 6.8 years ago • muc345
I noticed that if the GO term list is
re-ordered, then the value in the thousandths decimal place changes
(0.00X). I have tried several iterations of this now with the same
result.
Thanks for any insight you can provide.
Matt
Recent ...
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jwp48
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Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew,
We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
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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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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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…
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