months of graduation.
*The Telegraph
The University of Stirling is a charity registered in Scotland, number
SC 011159.
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to use PrepareAnnotationEnsembl() function in customProDB. Based on Ensembl's site the current dbSNP version for Macaca mulatta is snp131. However, if I try to enter that into the function I get an error.
<pre>
ensembl = useMart(biomart...splice_matrix = FALSE, dbsnp="snp131", COSMIC=TRUE)</pre>
I have also tried just using the number e.g. dbsnp="131". Both commands ret…
updated 10.4 years ago • kristenbeck527
rest of the columns are
fold
changes ( diseased/N) for diff sample sets ( Species=Human). The total
number of differential expressed genes are around 1200.
Please advice.
Thanks, Roopa
[[alternative HTML version deleted]]
</div
updated 12.0 years ago • Roopa Subbaiaih
Having successfully run analyzeChr() on chromosomes up through 22 and X (but not higher-numbered chromosomes, see <https://support.bioconductor.org/p/62551/>), I ran mergeResults() to move forward with analysis on...Having successfully run analyzeChr() on chromosomes up through 22 and X (but not higher-numbered chromosomes, see <https://support.bioconductor.org/p/62551/>), I ran merge…
updated 11.1 years ago • jessica.hekman
Dear Martin,
thanks a lot for implementing the awesome GSEABase infrastructure. Especially the conversion between identifiers is something I use a lot. So far, I had been annotating my GeneSet objects by referencing `` orgDb `` objects (e.g. `` org.Mm.eg.db ``).
Once I noticed that there are the `` OrganismDb `` wrapper packages as well (e.g. `` Mus.musculu ``s), I tried to use them in…
updated 8.4 years ago • sandmann.t
L3_D L3 No
L3_E L3 No
L3_F L3 No
My aim is to identify differentially expressed genes between healthy and disease samples for each one of the cell lines.
As I am not interested...apply here.
Pointers/advice would be greatly appreciated.
Thank you.
sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.…
The [emptyDrops][1] algorithm has been designed to identify cell populations with low RNA content which otherwise may be missed, especially in very heterogeneous samples...However, a known side-effect is that a higher number of low-quality cells may be recovered eg. droplets containing cell fragments, stripped nuclei and damaged cells, as
updated 20 months ago • rocanja
t see an answer
>to this, so perhaps someone can help.
>
>Limma uses a Printer Class to identify which print group a spot
>belongs to. This data object includes the number of grids, their
>arrangement and how
updated 19.2 years ago • Gordon Smyth
joining the two factors and using contrast to analyse these. This obviously will require a large number of contrasts to be made for all the genotypes.
<pre>
dds$group <- factor(paste0(dds$genotype, dds$treatment))
design...risk genotypes to pull out risk specific gene changes for these. I then am going to see how these identified genes change between other risk categorie…
<div class="preformatted">Dear all,
I am using limma package to identify differential expression. I have 5
contrasts, I used F-statistic to measure significant differential
expression, the F-test p-value is adjusted by "fdr" method . I used
the command
p.adjust(eb$F.p.value, method="fdr") < 0.05
where eb is the object from eBayes(). I got 397 significant
differential expression.…
<div class="preformatted">Dear all,
I have some basic statistical questions and which packages might
provide
tools to answer those.
I am running R 2.0.1 + Bioconductor under Debian testing.
I did have a look at the archives but did not find any satisfying
answers (or I didn't search the right way) and since I have only a
limited statistical background I need some pointers/help.
1.
I hav…
updated 20.7 years ago • A.E.Schiel@lumc.nl
0 1</pre>
And performed the analysis, using get.siggenes with vars=groups, to obtain a number of significantly-differentially-expressed genes for each comparison to the Control, e.g. sigs$sig.genes$ME49\_1.2vsControl...43 11 0 0 0 1 0</pre>
Here, I found that the genes identified as significant in this group were different…
updated 9.4 years ago • ls299
Can minfi be used for identifying differentially methylated regions for two samples having only one replicate each? Please suggest
updated 9.2 years ago • arisarkar88
annotation and Condition A causes a loss of one peak but retains the others, a difference may not be identified.
As a next step, I would like to use an undirected peak calling method, such as MACS2, to identify peaks in my dataset
attempting to use edgeR (3.12.1)'s glmTreat() function </span><span style="line-height:1.6">to identify genes that are significantly up-regulated by >2-fold in one group over another. My understanding from Sections...that are both up- and down-regulated. Is it possible to perform a more specific test in edgeR to identify just the significantly up-regulated genes above …
updated 9.5 years ago • le2336
Dear all,
I am using DESeq2 to identify differentially expressed genes between two conditions. This is a summary of my code:
dds-tvsc <- DESeqDataSetFromMatrix...function instead of p-adjusted values (FDR). As far as I understand, I have to check s-values to identify differentially expressed genes (as s-value is equivalent to FDR in the `results` function) ; however, I do not kn…
nbsp;
but I get the following error:
\`\`\`
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body...4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLI…
updated 10.0 years ago • rmporsch
div class="preformatted">Dear list,
I get an error:
"Error in contrasts.fit(fit,contrast.matrix):
Number of rows of contrast matrix must match number of
coefficients
In addition:
Warning row names don't match col names of...error message.
Any input would be greatly appreciated.
With thanks,
David
sessionInfo(): R version 2.8.0 (2008-10-20)
</div
updated 16.8 years ago • David Martino
the same:
```
> ###################################################
> ### code chunk number 20: edgeRstd
> ###################################################
> d.mont.std <- estimateGLMCommonDisp(d.mont, design = design)
> efit.std <- glmFit(d.mont.std, design...ve been using:
```
> ##############################################…
updated 6.0 years ago • Jenny Drnevich
confused with regard to a particular thing. At one place, it suggests that a correction vector is identified for a cell in the target batch which is an averaged correction vector from all MNN pairs of that cell with cells...in the reference batch. The MNN pairs help identify local variation in subpopulation of the target batch. But then the batch vector, the component of correction vector...becau…
updated 4.2 years ago • p.joshi
I am using limma to identify proteins that are differentially expressed in a tissue collected from four subjects at two different stages...I am using limma to identify proteins that are differentially expressed in a tissue collected from four subjects at two different stages. I...found 102 DEPs using approach 1 and 124 DEPs using approach 2, of which 101 were shared. Approach 1 identified 1 uniqu…
updated 5.8 years ago • jkhudyakov
<div class="preformatted">Hi,
I was trying to get significant KEGG terms for yeast. Previously, I
used the "YEAST" package, but I am now shifting to the "org.Sc.sgd.db"
package. A sample of the code, and the error I get is reproduced
below:
------------------------------------------------ Begin code
-----------------------------------------------------------------
## TEST HYPERGTEST FOR K…
I need to read in a number of idat files and quickly get their locations. The minfi function `read.metharray.sheet` does exactly what I need...I need to read in a number of idat files and quickly get their locations. The minfi function `read.metharray.sheet` does exactly what I need, but...define the search in *a different location* ?
[1]: https://www.rdocumentation.org/packages/minfi/versions…
updated 2.8 years ago • Diogenesis
retrieve the top genes (in
my
case, cause I am interested in subsequently doing GSEA analysis, I set
number=100) which are differentially addressed.
The question I have is how can I map the Affy ID which is found in the
results...that I can use to fetch annotations from a
post-Limma analysis?
My session info is as follows:
R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit…
updated 12.6 years ago • Jeremy Ng
unsure whether that is the intended behaviour and if so, what the
interpretation is.
Here are the versions I am using:
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] en_CA.UTF...and Comp5, but image2
shows
an intersection between Comp3 and Comp5.
My question is shouldn't the numbers agree between both venn diagrams?
Thank you fo…
<div class="preformatted">Hello everyone,
I'm trying to use biomaRt to simply get the Entrez Gene IDs from a
list of probe ids from the Affymetrix Mouse 430 2.0 chip. When I use
the getBM function, I end up getting a different number of rows in the
resulting table than I input. I've read the getBM help and searched
this mailing list, but to no avail. My code...from the Affymetrix Mouse …
<div class="preformatted">Hi all,
I need to normalize GFP expression by cell size and look at the
distributions for my data. After I created the new variable, and
tried to plot it using densityplot, I got a graph with the x and y
axis but no plot. After playing around with variations of the
function, it seems as if it doesn't like dividing any number by one of
the variables. I'm not sur…
<div class="preformatted">Hi List,
I'm trying to run an association analysis with GGTools. I'm getting an
error
when I run:
> outData <- gwSnpTests(gs1~male, hapSmlSet)
Error in data.frame(get(pname), pData(sms)) :
arguments imply differing number of rows: 0, 87
There are 87 samples in my analysis so that explains that, but I don't
know
what "get(pname)" is doing or why it …
I get
"Error in solve.default(xtx, xty) :
system is computationally singular: reciprocal condition number = 0"
When I use the default CDF (by not specifying a CDF when loading in
with ReadAffy()) fRMA works fine, so it seems like the...Is use of the alternative CDFs
supported with fRMA?
Thanks!
Adam Cornwell
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 …
updated 12.9 years ago • Cornwell, Adam
no better than
DESeq
at downweighting tags with extreme variances, or that this has to do
with
the number of replicates. While extreme cases like the example that
Laurant mentions may need special intervention, edgeR was...chosen prior.n to be lower than the default. The default
value prior.n=10 does result in tag1 being identified as
differentially
expressed. It is hard to give universal guid…
Hi TPP2D package maintainers,
I am trying to analyse data from a 2D-TPP experiment. Unfortunately, the following step returns an error:
```r
> null_model_B2 <- bootstrapNullAlternativeModel(df = preproc_df, params_df = model_params_df, B = 2)
[1] "Warning: You have specificed B < 20, it is recommended to use at least B = 20 in order to obtain reliable results."
|==…
updated 3.4 years ago • Tobias
I'm running a Deseq2 with RNA seq data to compare between test and control which every condition has 3 duplicated. But when I compare between test vs. control I got 1797 DEG but control against test I got 1760 genes.
```r
res<-results(dds, contrast = c("dex", "T0", "T20"),alpha = 0.05)
res2 <- lfcShrink(dds=dds, coef="dex_T0_vs_T20")
sig <- res2[ which(res2$padj &…
updated 4.5 years ago • ชัยวัฒน์
I have two biological questions that I would like to address:
__1) I want to identify genes whose values change significantly over time in one condition.
2) I want to identify genes who...lev)
design <- model.matrix(~0+f)
colnames(design) <- lev
fit <- lmFit(eset, design)
# identify genes whose values chan…
updated 8.5 years ago • relathman
AffyBatch object
size of arrays=744x744 features (23 kb)
cdf=HT_HG-U133_Plus_PM (54715 affyids)
number of samples=16
number of genes=54715
annotation=hthgu133pluspm
notes=
> featureNames(my.data) <- gsub("_PM","", featureNames...gt;
> Jim
>
>
>
> BioC_mirror: http://bioconductor.org
>> Using Bioconductor version 2.12 (BiocInstaller …
updated 12.4 years ago • steven wink
Error in easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens",
chr.sizes = "auto", :
The number of conditions: 0 did not correspond to the number of
samples: 1
In addition: Warning messages:
1: In easyRNASeq(filesDirectory...size list is not compliant. Correcting it.
2: In .Method(..., deparse.level = deparse.level) :
number of columns of result is not a multiple of vector length (arg
…
updated 12.2 years ago • Aki Hoji
<div class="preformatted">Bioconductors,
I am working on an Arabidopsis RNA sequencing experiment and have
run
into some trouble. I found that I was able to map ~94% of my ~35
million
reads / library to the Arabidopsis TAIR10 genome using tophat2 (100 bp
single end reads). After I counted my mapped reads I found that only
about
47% of my mapped reads were counted. I found out there is…
updated 12.3 years ago • Sam McInturf
<div class="preformatted">Dear list,
I noticed a strange distribution of q values after correcting a list
of
22960 p values with the q value package:
> qsummary(q)
Call:
qvalue(p = p, robust = T)
pi0: 0.07742146
Cumulative number of significant calls:
<1e-04 <0.001 <0.01 <0.025 <0.05 <0.1 <1
p-value 293 1067…
updated 20.1 years ago • Dr. Reinhard Hoffmann
the fields of the HyperGResult object. What I understood is:
o ExpCount: the expected number of genes in the selected
gene
list to be found at each tested category term.
o Count: for each category term tested, the...number of genes
from the interesting gene list that are annotated at the
term.
o Size: for each category term tested, the number.…
Hi,
Is it a way to identify significant interaction without replicate and inter-sample comparison ?
Thank you for your help.
Attis
 
updated 10.4 years ago • julienpontis
file
names from the sample sheet, and re-build the RGSet again? Similar
question goes to probes identified to have detection p-values higher
than 0.01, and CpGs in Chromosome X & Y. I think these CpGs should be
excluded...appreciate your help and wish you a happy holiday season!
Qin
-- output of sessionInfo():
R version 2.15.2 (2012-10-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
l…
updated 12.0 years ago • Guest User
use the xx output to gain information
(i.e.
tx_id, tx_name) about the feature which the function has identified as
nearest?
I would be happy to supply any more info as required
Tom
[[alternative HTML version deleted]]
</integer></integer
updated 12.8 years ago • Tom Oates
List,
I am working on a data set generated using Illumina's methylation 450K
array. The goal is to identify regions that are differentially
methylated between cases and controls. It seems that people are using
beta value...alternative HTML version deleted]]
</div
updated 14.0 years ago • Chen, Zhuo
<div class="preformatted">Dear All,
I hope to get some help on the hyperGTest in GOstats. I want to do an
GO enrichment anlaysis on a set of E. coli K12 genes (substr DH10B). I
attached the target id file, partial ecoli id file (as
universeGeneIds) and sessionInfo to the email. The following is my
commands and error. It seems that my gene id is not found in the
annotation package but I don…
updated 16.1 years ago • Yue, Chen - BMD
<div class="preformatted">Dear bioconductors,
I just installed the lumiHumanV1 package via the biocLite() procedure
yesterday. The identifiers of the single probes look very strange to
me.
Beside that they don't appear in the annotation file provided by
Illumina...bioconductors,
I just installed the lumiHumanV1 package via the biocLite() procedure
yesterday. The identifiers of the single…
updated 18.4 years ago • Benjamin Otto
of the BLAST when a new verion of
RefSeq is
out.
4) The potnetially cross-hybrdized probes are identified and
documented.
Cheers,
Simon
***************************************************
Simon Lin, MD, CSDP
Associate Director, Bioinformatics
676 N Saint Clair, Suite 1200...So I don't think the
lumiMouseV1 on the Bioconductor web site has the latest work???
How does your version differ to wha…
updated 18.6 years ago • Simon Lin
gene annotations across both studies. However, I have encountered several challenges:
The gene identifiers in the two datasets appear to differ, making it difficult to align them for comparative analysis.
I have attempted...am seeking guidance on the following:
1. What are the recommended approaches to standardize gene identifiers between these two datasets?
2. Which tools or packages a…
updated 12 months ago • Dhite
Hi everyone,
I am trying to upload a prefiltered data from Illumina HT\_12\_v4 beadchip. I have performed the normalization and differential analysis.
Now I want to do pathway analysis together with network anaylsis using PathVisio and Cytoscape.
Unfortunately the Ensembl bridge files :http://bridgedb.org/data/gene\_database/
http://www.bridgedb.org/mapping-databases/ensembl-gene-…
updated 8.0 years ago • p_donchev84
div class="preformatted">Greetings,
I am using the GOstats package to identify significant association
with GO
terms of a set of "interesting" sequences NOT identified by a
microarray.
As far as
updated 18.7 years ago • Michael Mayhew
edgeR with known annotations taken from a database.
After completing this, I decided to set off identifying novel transcripts (novel ncRNAs) and antisense transcripts. It is my intention to quantify them and determine...extra genes in any way skew the data such that genes (from known annotations) that were previously identified as DE are not anymore? Should I just be filtering for novel and anti…
because as it mentions "
l__umiHumanAll.db is using or is likely to need access to special nuID identifiers. Users can learn about these identifiers from vignette documentation provided with the lumi 
updated 10.5 years ago • svlachavas
gene level, RATs compares the set of each gene’s isoform abundances between the two conditions to identify if the abundance ratios have changed. At the transcript level, RATs compares the abundance of each individual transcript...against the pooled abundance of its sibling isoforms to identify changes in the proportion of the gene’s expression attributable to that specific transcript.
I don't …
updated 6.4 years ago • UserAnonyme
package that the SpeCond method uses to fit a
mixture of normal distribution.
I restricted the number of normal (or component) to be tested from 1
to 3.
By default if the best model is found at the min or max number of the
component...testing only 1 to 3 components makes sense,
according to the pattern the method is looking for to identify
specifically
expressed gene/probes. I should probably add…
mydata.raw
AffyBatch object
size of arrays=640x640 features (64005 kb)
cdf=MG_U74Av2 (12488 affyids)
number of samples=20
number of genes=12488
annotation=mgu74av2
# R 1.9.0 beta package versions
base 1.9.0
utils 1.9.0
graphics...1.2-1
splines 1.9.0
matchprobes 1.0.2
mgu74av2cdf 1.4.3
mgu74av2probe 1.0
# R 1.8.1patched package versions
base 1.8.1
ts 1.8.1
nls 1.8.1
modreg 1.8.1
mva 1.8.1
ctest…
<div class="preformatted">Hello bioC users,
as you can see below, this was posted over a year ago. Unfortunately I
tried the same today and for some mysterious it is not working
correctly
any more.
What I have is the same data.frame:
> dat
id flybasename_gene flybase_gene_id entrezgene
1 1616608_a_at Gpdh FBgn0001128 33824
2 1622892_s_at CG3…
<div class="preformatted">Hello all,
I am looking to identify common expression profiles (signatures)
across many different pairwise comparisons. Essentially, I have lots
of diverse affymetric data sets from different tissues, but for each
tissue type I have one sample that expresses my phenotype of interest,
and one or more others that do not. I am interested in identifying
which mRNA tr…
compare differential expression between two cultivars, and two timepoints. My goal is primarily to identify the differentially expressed genes between the two cultivars, two timpoints, then also identify the genes that...5DAP
cultivar A, 5DAP vs cultivar B, 14DAP
cultivar B, 5DAP vs cultivar B, 14DAP
and also identify those genes with signficant interaction
updated 5.1 years ago • sokumoto
and Hs.479995 is NANOGP1
(Nanog homeobox pseudogene 1) and they both have the same
LocusLink identifier and share some GB identifiers
so, is 220184_at a probe with 2 UniGene identifier ?
I appreciate any comment .
Mayte
updated 21.3 years ago • Mayte Suarez-Farinas
I recently posted a question regarding [identifying GO terms that were mapped to GOslims and received a great answer on how to do this.][1]
[1]: https://support.bioconductor.org...I recently posted a question regarding [identifying GO terms that were mapped to GOslims and received a great answer on how to do this.][1]
[1]: https://support.bioconductor.org/p/128407/
However, in th…
updated 5.8 years ago • samwhite
Hi,
I'm having trouble interpreting the intended effect of the absRanking argument on GSVA. I'm running an example with three gene sets, one is strongly positive, one is strongly negative, and one without differential expression.
Standard GSVA (absRanking=FALSE) returns the expected results (up/down/none), but GSVA with absRanking=TRUE does not show any significant enrichment. My ultimate a…
updated 18 months ago • gad.abraham
to download package pd.hta.2.0 with no success. I have tried on multiple computers, different R versions (4.0.3 & 4.0.4 respectively), different internet sources, etc. I continually get a timeout message. I haven't on my...package, which in my case is pd.hta.2.0
```r
BiocManager::install("pd.hta.2.0")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing…
updated 4.8 years ago • croft.carys
Recent ...
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