and want to
use
DESeq2 to normalize the counts. However, I used Picrust to correct the
16S
copy number for OTUs and the number generated by this correction are
not
integers (but decimals). Can I used DESeq2 to normalized...my count data
(using size factor) obtained by this 16S number correction considering
that
the DESeq2 was developed based in counts and not in counts corrected
by 16S
copy numbe…
Order by: Relevance
Hi there,
I am trying to analyse a data set to identify differentially expressed genes between plant development stages. Currently, I have generated the data for the...have less than 10 reads, rowSums calculates the sum of rows of a matrix or an array, counts is the number of occurences)
dds <- ddsHTSeq[keep,] # This removed ~10 000 elements, reducing size of matrix
dds$Stage <…
updated 3.8 years ago • cicely.day
div class="preformatted">Hi Mustapha,
I made the same erroneous conclusion in regards to software version
numbers. As I was told, they are NOT decimal places, so since 10 > 9,
R version 2.10 IS > 2.9. Which part of the version number...is
increased for a new version depends on the amount of change from the
previous version. There has to be some sort of major change to
increase …
updated 16.0 years ago • Jenny Drnevich
<div class="preformatted">
Dear Gurus,
I am doing an Illumina microarray analysis. The study design is a 2x2
(i.e. varying 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.
The problem is that after performing the GO …
updated 12.9 years ago • Guest User
Please Help! Why does getGEO return "Error: Duplicate identifiers for rows"?
How can this error be fixed? This getGEO command was working fine for a week and then Stop working...R\\\\desktopBrstC")
Found 1 file(s)
GSE76275\_series\_matrix.txt.gz
Using locally cached version: D:\\I\_\\\_Gene\\R\\desktopBrstC/GSE76275\_series\_matrix.txt.gz
Error: Duplica…
updated 8.1 years ago • cg
for org.Hs.egENSEMBL:
org.Hs.egENSEMBL is an R object that contains mappings between Entrez
Gene identifiers and Ensembl gene accession numbers.
Help description for org.Hs.egENSEMBL2EG (it is the same help
message):
org.Hs.egENSEMBL...is an R object that contains mappings between Entrez
Gene identifiers and Ensembl gene accession numbers.
Help description for org.Hs.egSYMBOL:
org.Hs.egSYMBOL i…
updated 13.1 years ago • John St. John
a command or a package that can
help me to retrieve the aminoacid sequence starting from the protein
identifier, through a link with Uniprot or similar:
Let's say I have :
P10451 , Human
I would like to obtain:
MRIAVICFCL LGITCAIPVK...self.aspx/le%20PV%20in%
20viaggio!/89.JPG
[[alternative HTML version deleted]]
</div
updated 16.5 years ago • Giulio Di Giovanni
and SingleR packages to analyze my scRNAseq data. Everything works well and I was able to identify cell types in my samples with the following
pred <- SingleR(test=merged, ref=ref, labels=ref$label.main)
I am looking...for a way to look deeper and identify T cell subsets. any advices or suggested tutorials?
thank you
updated 5.0 years ago • achaillon
Hi,
I am trying to use the Bioconductor package in R 3.6.3 on Windows 64-bit platform to analyse my RNA-seq data with Apis mellifera.
I am facing difficulty from an error described below. I have checked the available GTF file, using readGFF, the gene_id comes in the 10th column. But that is how I have downloaded the file from:
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/254/395/GCF…
updated 5.8 years ago • chatterjee.arumoy
5 males and 5 females for 4 tissue types (skin, liver, brain, and gonads), and I would like to:
1. Identify genes/transcripts with skin-biased expression
2. Identify genes/transcripts with sex-biased expression
3. Identify...look better)
I then fit the model using glmQLFit:
```
fit <- glmQLFit(y, design)
```
To identify skin-specific genes, I then do:
```
skinVbrains <-…
updated 6.4 years ago • spflanagan.phd
X=1, then all the (merged) peaks are
included in the consensus peakset. If X=2, only peaks that were
identified in at least two of the samples are included. In the
vignette example where there are 11 samples, setting X=11 would...only
analyze peaks that were identified in all 11 samples.
You can see how many peaks would be in each possible consensus peakset
defined using minOverlap...and how thi…
Bioconductor. Now, I
want to
add a column in the final output, which includes the gene accession
number
of reference sequence, for example, NM_008725 besides gene entrez ID
and
gene name. In this way, I could match probe ID...to their corresponding
accession number.
But how can I write a code to implement it?
Thanks in advance.
YiSong
PS.
library("annotate");
library("mouse4302.db");
tota…
genes and
comparing the resulting list to the gene universe will enable the
testing procedure to identify regulated ontological processes, but it
won't be able to identify whether the processes are upregulated or
downregulated
div class="preformatted">Hi,
Is it normal not to have the same number of sequences in the fastq
file and the object generated from readfastq?
grep @ SRR062641.filt.fastq | wc -l
187786
 ...nbsp; S4
Thanks,
Carol
[[alternative HTML version deleted]]
</div
updated 12.7 years ago • carol white
Hi all,
I am trying to use PEER in R (on conda) to identify hidden confounders in the raw counts of my RNA-seq experiment. I am following their tutorial ( https://github.com/PMBio...I have installed R-PEER on Conda, but am having issues with following with the PEER pipeline, to identify 10 hidden confounders in my expression data. I was wondering if anyone could advise? I couldn't find much he…
updated 6.9 years ago • rodrigo.duarte88
with different subsets of the same data:
subscript out of bounds
arguments imply differing number of rows: 4, 6, 2
argument of length 0
arguments imply differing number of rows: 0, 8
As with these arguments it works depending...keepCol)[i])
}, error = function(e){message(e)})
</code></pre>
I am using the latest R 3.4.2 version and the latest Bioconductor ver…
updated 8.1 years ago • Lluís Revilla Sancho
analysis was done using Deseq2 v1.2.10 and R v.3.0.2. Although we are still using the same version for Deseq2, R on our system is now upgraded to 3.2.1. Repeating exactly same analysis using the same code but with newer...version of R, gives me half the number of genes as significantly expressed.
Does anyone know why this discrepancy could
updated 10.2 years ago • genomica
preformatted">Hi,
The maPalette() function (in the marray package) does not always
return the number of colors requested. More specifically, if a middle
color is given and the number of colors requested is odd, then
maPalette...returns either one more or one less than the requested
number of colors:
# >>> returns 12 colors <<<
maPalette(low="white", …
3/2/2013 8:20 AM, Anirban [guest] wrote:
> Dear all,
>
> Is there any way to get all entrez identifiers that are annotated
with KEGG pathways? Actually I am using GOStats package in R to
perform KEGG pathway enrichment...In general, for each KEGG
pathway term there is a list of annotated hgnc symbols or entrez
identifiers.. For all KEGG pathway terms we must have one list of
…
4756990164 9130 6715201209
JJJ 1434 4756996655 1602 6715208737
Where the 1st column is the identifier, the 2nd column =
observations 1, the
3rd column = background counts 1, the 4th column = observations 2
and the
5th column...c(as.integer(data[i, 2:5])), nrow = 2) :
NAs introduced by coercion
When I replace the large number in the 3rd and 5th column with
smaller
numbers, the…
updated 12.5 years ago • Gibbons, John G
<div class="preformatted">It looks like Biostrings function "writeFASTA" overwrites the output
file at each run.
It seems it does not support the "append" parameter.
I have to generate one big file gathering a miRNA identifier and
relative sequence followd by a variable number of dara records
pertaining such a miRNA target genes transcription.
Each record is made up of a 3'utr identifie…
updated 16.5 years ago • mauede@alice.it
file that has not been preprocessed
fully.
However, perhaps because of minor changes, the resulting number of
probes
excluded changes from what I had documented in the past (using the
same
script).
It seems my path forward should...be to use an older version of lumi
(where
can I find this) and try and see if that gives me the same number as
before. How can I install this older version...Thanks,
…
I'm developing a new gene expression and survival analysis platform based on Bioconductor, but also including the custom annotation products from the BrainArray lab - http://brainarray.mbni.med.umich.edu - which could potentially become the new standard for some widely used microarray platforms. More use would also be made of the Gene Ontology, moving away from an emphasis on individual&…
updated 11.2 years ago • robin073
in the range of 13-17 million
reads.
I was wondering if DESeq can handle this kind of difference in number
of
reads between samples? Or a down sampling of reads is necessary
before
DESeq?
Regards,
Rushiraj
[[alternative HTML...version deleted]]
</div
<div class="preformatted">Hi All,
Is there a way to identify the genes that contribute to the gene set
enrichments calculated by roast/romer? I realize that all of the genes
in...div class="preformatted">Hi All,
Is there a way to identify the genes that contribute to the gene set
enrichments calculated by roast/romer? I realize that all of the genes...a
gene
set, or something else alto…
updated 11.9 years ago • Stephen Hoang
Hello,
I have a question about identifying highly variable genes after applying vst from deseq2. I don't think it makes much sense to find those genes after...variance stabilization. Should I identify the genes using counts or normalized counts and directly use the gene list on the post-vst data for any downstream
updated 2.5 years ago • MaXXinE
<div class="preformatted">Hi everyone,
I am working with mRNA data from Affy 'drosophila2' arrays and miRNA
data from Affy 'mirna3' arrays. I have identified a list of
differentially expressed mRNAs and miRNAs. I'm having a bit of trouble
with some downstream analyses and I'm hoping someone might be able to
offer some help.
I would like to use my list of differentially expressed miRNAs to…
cancer in TCGAbiolinks.
1 file is downloaded. In the file I get with TCGAbiolinks, samples are identified
with designations such as 75a8bcb9-cac9-4fee-8757-bb802f4d355f", and copy
numbers are identified by -1,0,1.
When I...use the TCGA web interface samples are identified by their sample numbers,
and copy numbers are denoted by their actual inferred copy number 1,2, 10 etc.
However they...xlsx)…
updated 4.2 years ago • raf4
<div class="preformatted">Hello All,
I am using DESeq for identify differentially expressed genes among a
couple
of samples. At the end of the calculations i write the results to 3...div class="preformatted">Hello All,
I am using DESeq for identify differentially expressed genes among a
couple
of samples. At the end of the calculations i write the results to...last two lines of
code
…
<div class="preformatted">Hi, I am new to bioconductor. Is there a good package/work flow that
does copy
number/LOH analysis for Affy 100K chips, starting from CEL files? I
have 100K
data from ~ 30 tumor samples; and I plan to download 100K trios data
(90 healthy
individuals) as normal references from Affymetrix website. Do I really
need
normal references for copy number/LOH analysis? Cheng…
am using reactome.db for over-representive enrichment test, so I
wonder how I can get the total gene number for a given species in
reactome.db. For example, how many human genes (unique Entrez Ids) are
annotated in reactome.db...Is there any simple way to get this number
besides counting the shared genes between the annotated genes from
"reactomeEXTID2PATHID" and records from "org.Hs.egUNIGENE2EG…
gt; exprs.rawData <- exprs(rawData)
However, extracting the data itself gives me a different number of
rows:
> length(pNames)
[1] 243982
> dim(exprs.rawData)
[1] 292681 6
Ive verified that this result occurs using the sample...http://www.affymetrix.com/Auth/support/downloads/demo_data/mirna_3_sam
ple_data.zip
Shouldnt the number of probes in the CEL file be the s…
Is there a R package to identify long stretches of gaps (Ns) in human genome (hg19
updated 8.1 years ago • addyS
it
on my computer?
I am running R2.3 on Mac OSX. I downloaded the source file
for the latest version of the moe430a (moe430a_1.12.0.tar.gz)
and tried to install it from the R menu.
When I do library(moe430a), and moe430a...moe430a()
Quality control information for moe430a
Date built: Created: Sun Mar 26 00:22:20 2006
Number of probes: 22690
Probe number missmatch: moe430aACCNUM; moe430aCHRLO…
updated 19.7 years ago • MARIA STALTERI
RNA-seq data???, gene
FBgn0004449 is on reverse strand and the plot result shows that exonic
part number is aggregated from right to left (bigger coordinate to
smaller). But in vignette of DEXSeq for version 1.6.0, the example...gene used for plot, FBgn0010909, is also on negative strand but the
exonic part number 1 starts from leftmost. For me I think first
consequence is better to help me corre…
step 2
sudo apt-get install gdebi-core # step 3
export R_VERSION=4.3.3 # step 4 - notice version number is latest version always for first installation
curl -O https://cdn.rstudio.com/r/ubuntu-2204/pkgs/r-${R_VERSION...bin/Rscript /usr/local/bin/Rscript # step 9 - create Rscript symlink (first installation only)
R --version # step 10 - verify R symlink
Rscript --version # step…
updated 20 months ago • BioinfGuru
I would like to limit the number of displayed genes (so **not** the categories, which is easily done with showCategory) in the enrichplot heatplot, but have...Function to get my enriched gene sets and then passing that to heatplot. I don't want to limit the number of genes before the gse analysis itself and I also don't want to change the number of the maxGeneSetSize, but would like...ENSEMBL')
h…
updated 3.0 years ago • Melanie
div class="preformatted">Hi every body,
I'm just wondering about the current upgrading of R versions.
Actually, I have the R version 2.9, but the new version (R 2.10) is
already
availaible.
Theoritically, a new version is...usually higher in number than the
previous
one, but in R versions this is not the case ! Since 2.10 (newer
version
edition) is lower than 2.9 (older...version) !
So, is th…
updated 16.0 years ago • Mustapha A.
Hi everybody,
I'm using DESeq2 through phyloseq to identify bacterial OTUs that are significantly differently present between treatments. Yesterday I updated R and all...Hi everybody,
I'm using DESeq2 through phyloseq to identify bacterial OTUs that are significantly differently present between treatments. Yesterday I updated R and all my...Hi everybody,
I'm using DESeq2 through phyloseq to id…
div class="preformatted">Hi all,
I am comparing a number of cell types, and am wanting to find the
signature
genes of each cell type. I used the limma package to do this. The
signature...or other
BioConductor
package to do this.
Thank you in advance,
Wendy
[[alternative HTML version deleted]]
</div
preformatted">
Hi,
I'm trying to create a custom annotation package for arabidopsis using
RefSeq identifiers with AnnotationDbi's function makeDBPackage.
Everything runs smoothly but the generated package is empty...id type present in the fileName
gb/ug/eg/refseq/gbNRef
outputDir="doc/arabidopsis.anno",
version="1.0.0",
chipName="arabidopsis"
)
One strange thing here is that if I try t…
updated 15.0 years ago • Asta Laiho
clusterProfiler to do gene enrichment for a non-model species. After I annotated my gene sets to K numbers, I noticed different genes might be annotated as the same K number. Should I get the unique K number set to do gene enrichment...or use all K number to do functional enrichment? Will this influence my result?
And I also need to get the K number for my whole genome to make...it as the back…
updated 5.0 years ago • XM
control="no interest",
statCalc="arith", hkgCalc="arith")
Error in caseM[hkgs[1], ] : incorrect number of dimensions
Apart from the vignette, I didn't think I would need to identify hkgs
in each sample??
What is odd is that I...me where I'm wrong.
Respectfully,
Franklin
-- output of sessionInfo():
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)
…
replications each, essentially a 2x2 factorial experiment with 4 replications.
Now we want to identify genes that are uniquely upregulated and downregulated in both genotypes under drought. Specifically...we want to identify unique genes in the QTL region of the very drought tolerant genotype that are upregulated and downregulated. ...expressed genes (DEGs) be…
updated 7.6 years ago • tarun2
Hi,
I'm using EBSeq-HMM to find DE genes. The problem is among 17611 genes, 16139 genes are identified as DE which is very unusual.
My cutoff to filter genes out before detecting DE genes was to discard all those genes...model, I have to run this model by its default settings.
What do you think accounts for this large number of DEGs found? Has anyone worked with this package before? I read the…
updated 8.9 years ago • fa.gholizadeh89
I am getting an error while mapping the gene names to the StringDB identifiers using the map function. The code was working fine before with the StringDB version 11 but giving an error for version...I am getting an error while mapping the gene names to the StringDB identifiers using the map function. The code was working fine before with the StringDB version 11 but giving an error for version 11.…
were collected at 4 different time points,
which algorithms would you recommend in order **to identify the trends ?**
thanks a lot,
-~ Bogdan
However due to the design of the snp.matrix it cannot
store
these log2ratios and associated Copy number. Is there an available
package/class out there that has been created. I have spent some time
looking at the bioconductor...list and can't seem to find one? Could I
in
theory alter the smlSet class to stored my own version of snp.matrix
instead?
Many thanks in advance,
Nathan
[[altern…
preformatted">Dear Bioconductor community,
I am looking for a package that does Copy number along with LOH
analysis (B allele frequency) for intensity files from SNP 6.0 arrays.
Please direct me to the right package...for this kind of analysis. Thank
you very much in advance
Raj
[[alternative HTML version deleted]]
</div
<div class="preformatted">Dear Dennis,
To find transcripts specific to one tissue versus the others, you need
to
test that tissue vs the others, but I'm sure you already know that.
If
you have replicates of each tissue, you can do pairwise comparisons
between the tissues, and choose transcripts which are consistently up
in one vs all the others. If you don't have replicates, there's no
al…
<div class="preformatted">
I'm getting an error that says "incorrect number of dimensions" when I
try to use parLapply on a function that works fine on a single non-
multicore node. I see that bug fixes...div class="preformatted">
I'm getting an error that says "incorrect number of dimensions" when I
try to use parLapply on a function that works fine on a single non-
multicore node. I se…
updated 12.2 years ago • Guest User
I had already posted that repository to your tracker. So, please help me solve it and link the new version of PhosMap to issue number 953. Many thanks
updated 7.0 years ago • ecnuzdd
<div class="preformatted">Hi,
I currently have a list of HUGO gene ids which relate to genes in
areas of gain over a whole chromosome, and would like to perform GO
enrichment analysis on them. So I have 2 problems:
1. currently i have been defining my gene universe based on affymetrix
arrays, however now I am working over the whole genome. gene_universe
= getBM(c("entrezgene"), mart = ens…
updated 17.3 years ago • Nathan Harmston
pre>
Hi,</pre>
I have issues with the getIndices() function from the flowWorkspace package. It identifies much more cells as "TRUE" for a gate than it should. Here's my code:
<pre>
wspath<-"~/Desktop/workspc.wsp"
ws<-openWorkspace...lt;-nodelist[num_f5]
summary(getIndices(G[[1]],f5))</pre>
I have no clue why getIndices() doesn't identify the right cell…
updated 8.9 years ago • helena_t
I am doing transcriptome analysis of a non-model plant species. Is
anyone can help me to get TAIR identifiers corresponding to my
sequences? I have to blastx more than 20000 sequences.
My input data is a fasta file containing...Vol 112, Issue 8
> ********************************************
[[alternative HTML version deleted]]
</div
updated 13.6 years ago • Hers
my microarray data using limma and I'd like to ask a question. What is the best way to reduce the number of differentially expressed genes? As you can see below, I have used the ___treat______ method___ to reduce it...a plot to represent of differential expression results ( Figure Contrast(3)), it is possible to identify significant genes. So, Why does it happen? Sorry …
updated 8.3 years ago • Sanches
1.6">Hi,</span>
Somatic signatures package uses RSS and unexplained variance to assess the best number of signatures. In Alexandrov et al paper (Cell Reports 3, 246-259) they used cosine similarity and Frobenius reconstruction...error to determine the number of signatures.
Did any one compare the two ways and find difference in determination of number of signatures?
Thank
updated 10.4 years ago • Asma rabe
I'm looking to retrieve metadata for all versions of each package, including their dependencies, from Bioconductor. Specifically, I need this data in a structured...JSON format that includes project names, version numbers, and corresponding dependencies. I am aware of the Bioconductor API but am unsure of the best way to use it to
updated 17 months ago • Sadman
I've plotted pca plots with just using the plot() function as well,
but I still do not know how to identify the particular sample that is
the outlier.
Any ideas for both affycoretools() or the general plot() function will
be
updated 13.2 years ago • Guest User
Li, Hua wrote:
> Hi, Francois,
> Yes, if I know one protein in a specific pathway, how to identify
> all the other members?
> I appreciate your help!!!
> Hua
>
> ________________________________
>
> From: Francois...Li, Hua
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] how to find the children identif…
updated 18.6 years ago • Francois Pepin
Recent ...
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