div class="preformatted">Hi
I am running Windows XP, R version 1.7.1 and Bioconductor 1.2,
installed about 2 weeks ago from the website. I am getting some
errors with maPlot from...the nature
of the data set that doesn't exist...?? Or perhaps the default range
is greater than the number of valid data points???
As an aside, I opened up the same data using the limma module and
using the plot…
Order by: Relevance
Dear Bioconductor community,
while trying to utilize the MultiAssayExperiment data container, along with a specific queried TCGA dataset, to perform some initial filtering and data cleaning prior downstream analysis, I have encountered the following error when tried to add an additional omics layer to the MAE object:
```r
library(MultiAssayExperiment)
library(curatedTCGAData)
library(…
updated 5.0 years ago • svlachavas
Hi all,
I downloaded the STAD project 450k methylation data.
The version reported is "Data Release 39.0 - December 04, 2023"; the Samples dataset size is 397.
Unfortunately what I'm noticing is...that there is a large number of NAs;
for example on the first and on the second Sample the NAs table are
1st)
```r
FALSE TRUE
412169 73408
```
2nd)
```r
FALSE TRUE
updated 21 months ago • Giovanni Calice
wether it would change the results if we provide the
initial library size, the mapped reads number or just the sum of
counts to perform an RNAseq analysis,
thanks in advance,
anna
-- output of sessionInfo():
R version 2.15.1
gt; 95% Query coverage and >90% identity.
Is there program in R to select them? I want to detect number of
organism showing uniques results for given sequences.
Thanks.
Dr. Ghorpade Prabhakar B.
PhD Scholar ( Veterinary...Biochemistry),
IVRI,
Izatnagar,
Bareilly, U.P.,
India
[[alternative HTML version deleted]]
</div
22300 genes
42 samples
phenoData object with 1 variables and 42 cases
varLabels
sample: arbitrary numbering
> library(genefilter)
> f1 <- pOverA(0.25, lob2(100))
> f2 <- function(x)(IQR(x) > 0.5)
> ff <- filterfun(f1,f2)
> selected...function "lob2"
Can someone point out to solve this matter?
Thanks,
Lana
[[alternative HTML v…
updated 20.7 years ago • Lana Schaffer
the difference between p-adjust and
p-value?
when I use p-adjjust < 0.1 as threshold, I get a few number of genes,
while
in the case of p-value < 0.05, I get ,much more genes. I was wondering
which threshold is more accurate?
Sincerely...Biology (GBCB) PhD Student
Virginia Tech
Blacksburg, Virginia
[[alternative HTML version deleted]]
</div
the contrasting variable.
This is a little surprising since I'd expect log2foldchange to be a
static number when comparing two conditions, and the contrasting
variables only dictate testing for significance, ie., p-value.
Thank...you in advance.
-Rob
[[alternative HTML version deleted]]
</div
<div class="preformatted">I'm trying to follow up on the discussions by Laurent and Issac, b/c
we're also trying to run a lots of arrays (~200 133A) with
Bioconductors. We tried with R on our 32 bits Linux server with 2G
ram and it failed. So, my questions are:
1) now what is the highest number of chips you can process with
Bioconductor?
2) How do you know if your R is 32 bits or 64 bits …
updated 22.8 years ago • Shi, Tao
<div class="preformatted">Hi list,
I am working with a network, in a table form like this:
Gene1 Gene5 0.76
Gene1 Gene79 0.89
Gene2 Gene8 0.97
...
Basically, each row represents two genes that interact, and their
pearson
correlation coefficient (from 0.7 to 1).
What I want to get is a plot representing how the number of nodes and
edges
(separately) decrease…
called write.fasta, which works fine,
except for one crucial point:
there's supposed to be a maximum number of characters per line (the
default is supposed to be 60), but when I call the function, it simply
prints the entire sequence...argument)...
Anybody else experiencing this or have a solution?
I'm using Windows 7 64-bit, R version 2.10.1.
Regards,
Jonathan
</div
updated 15.8 years ago • Jonathan
and bioconductor again.
> library("seqinr")
Warning message:
package 'seqinr' was built under R version 2.8.1
> sessionInfo()
R version 2.8.0 (2008-10-20)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE
updated 16.8 years ago • Daren Tan
hgnc_symbol"),filters="affy_hg_
u95av2",values=c("1939_at"), mart=human.ensembl,verbose=TRUE)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query>
<query count="0" datasetconfigversion="0.6" requestid="biomaRt" uniquerows="1" virtualschemaname...filters = "affy_hg_u95av2", :
The query to the BioMart webservice returned an invalid result: the
number of columns in the result tab…
gt;Subject: R: [BioC] Pathway Information
>Date: Thu, 16 Jun 2005 17:43:49 +0200
>MIME-Version: 1.0
>Content-Transfer-Encoding: quoted-printable
>X-Priority: 3 (Normal)
>X-MSMail-Priority: Normal
>X-MimeOLE...tests=AWL,BAYES_00
autolearn=ham
version=3.0.1
>
>Sorry but it doesn't work:
>
>> get(paste("hsa", get("Biosynthe…
updated 20.5 years ago • John Zhang
<div class="preformatted">i'm trying to install the "Rbowtie" package of bioconductor. I'm
running R in root mode on ubuntu 12.4 LTS with the latest version of R
(3.1.0).
I follow the instruction on Rbowtie page :
source("http://bioconductor.org/biocLite.R")
biocLite("Rbowtie")
I...the "Rbowtie" package of bioconductor. I'm
running R in root mode on ubuntu 12.4 LTS with the latest version…
Dear all,
Users of the affy packages will have certainly noticed that the
'development' version has been through various stages of stability.
In some case I even advertised for functions, but in many cases
by the...of the package (we wished we would have done it
earlier,
but time... time...). Starting with the version number 1.2.1(***), the
package you will find on the web passed these tests.
Pl…
updated 23.3 years ago • Laurent Gautier
I generated a count list using featureCounts of my ATAC-seq data and fed it into R. I got the GC bias and lenght for each peak queried, and made a list for the sequencing depth. When I run the following command:
atac_counts_cqn <-
cqn(ataccounts0715,
x = ataccovar3$gccontent,
lengths = ataccovar3$length,
sizeFactors = atac.sizefactor,
verbose = TRUE)
I …
updated 6.4 years ago • Eric.Martin
Warning message:
In fun(libname, pkgname) :
mzR has been built against a different Rcpp version (1.0.10)
than is installed on your system (1.0.11). This might lead to errors
when loading mzR. If you encounter such issues...please also include the results of running the following in an R session
sessionInfo( )
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Runn…
count table used in DESeqDataSetFromMatrix. I have also spot checked some of these files, and the numbers within the individual file match what is in the geneCounts data.frame.
I have entered the code below. Any help would...2] see 'independentFiltering' argument of ?results</pre>
<pre>
SessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit…
updated 8.0 years ago • jillian.waters
div class="preformatted">Hi!
I'm using flowPeaks in combination with flowCore and flowViz to
identify clusters in flow cytometry data. I can get adequate
clustering of my flow frame, and now I want to get summary statistics...for each identified cluster (median fluorescence intensity for each
parameter etc.). I can't find any way of subsetting my flow frame
Hello
I'm currently working with methylation data from a number of studies (all 450k arrays). I have IDAT files for most, although a few only supply methylated/unmethylated signals...Hello
I'm currently working with methylation data from a number of studies (all 450k arrays). I have IDAT files for most, although a few only supply methylated/unmethylated signals on...from…
based on EnhancedVolcano plots after using DESeq2. I have 4 groups to compare. Showing 1 comparison identifies 3 significant DE genes.
when I plot the enhanced Volcano plot I find more genes in it. As far as I understand the padjusted...pvalue < 0.0001 & abs(PEG_EV_treatment_vs_POS_FBS$log2FoldChange) >= 1),]
print("Number of significantally DE genes DE group_POS_FBS_…
updated 5.7 years ago • rimss.khurana
nbsp;
for selection 1)
"0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1" (dimensionality is 19 as the number of classes)
and for selection 2)
"0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0"
selection 3)
"0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1"
and selection...the different (4) classes. We used a threshold of 0.9 for the correlation coefficients in order to identify only ge…
updated 10.6 years ago • arrigonialberto86
study
performed ) Can I group it based on patients (sampleNames) instead ?
2.How do I choose the number R (number of signatures to obtain) ? I
guess it should be less than number of columns of sca_occurances ? In
a recent publication...with 52 patients), they
mention - the have found two signatures, does it mean they have set
the number of signatures (R argument in nmfSignatures()) to 2?
My apo…
updated 11.5 years ago • Guest User
string
> with embedded nuls Warning: file ‘2a8c7fc7412c_file2a8c77d1db9c’ has
> magic number 'X' Use of save versions prior to 2 is deprecated Error
> in load(bfc[[rid]]) : bad restore file magic number (file may be
> corrupted
updated 3.3 years ago • davide.chicco
gt; Data
AffyBatch object
size of arrays=712x712 features (18 kb)
cdf=Zebrafish (15617 affyids)
number of samples=32
number of genes=506944
annotation=zebrafish
notes=
> qc<-qc(Data)
> plot(qc)
Error in rbind(c(), (vals[, p3] - vals...5: ratios(x)
4: ratios(x)
3: plot.qc.stats(x, ...)
2: plot(qc)
1: plot(qc)
> sessionInfo()
R version 2.5.0 (2007-04-23)
x86_64-redhat-…
updated 18.6 years ago • Georg Otto
gt; BCR
AffyBatch object
size of arrays=640x640 features (51204 kb)
cdf=HG_U95Av2 (12625 affyids)
number of samples=16
number of genes=12625
annotation=hgu95av2
> exprs(BCR)[1,]
H H H H H H H H H H H H H H
H H
687 859 883 608 711 567 827...new to this area. any suggustion will be appreciated.
regards,
w.f
[[alternative HTML ver…
colnames(Detection(BSData)) <- sampleNames(BSData)
Many thanks!
Cei
> sessionInfo()
R version 2.8.0 (2008-10-20)
i386-apple-darwin8.11.1
locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
attached base...Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2…
updated 17.0 years ago • Cei Abreu-Goodger
help.search for something in the R base package
> help.search("Control")
Error in rbind(...) : number of columns of matrices must match (see
arg 203)
In addition: Warning messages:
1: No Rd contents for package 'gregmisc' in...3. traceback of the latest error produces a very long list (aprox.
1.7MB) I
am attaching a zipped version.
4. Removing the GO directory restores the help.search fun…
updated 20.7 years ago • Gerard Tromp
but tried to follow the install instructions
to get DEXSeq. It seems to be installing the latest version but as
seen in the sessionInfo it shows an earlier version number. When
trying to use it cannot find the functions for...gt; DEXSeqDataSetFromHTSeq
Error: object 'DEXSeqDataSetFromHTSeq' not found
> sessionInfo()
R version 3.0.3 (2014-03-06)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
…
and I
> always get the same problem. I am using R 2.2.1 and I updated my
LIMMA to
> the last version today.
Actually you're using a version of R which is about 15 months old, so
you're getting an older
version of limma as...well. The only way to get the latest version of
limma is to use the current
version of R.
I don't know what problem you have here exactly, without knowing you…
I think it is supposed to be the
second
> column:
Ting-Yuan
There is a problem with using the IDENTIFIER column--it doesn't need
to be
unique and the geneNames for an exprSet do need to be unique. ID_REF,
on
the other hand...for the typical affy GDS, includes
affymetrix
probeset ids; that is the reason for using it over the IDENTIFIER
column.
If you know that the identifier column IS un…
you for advance for your answer and your help.
------------------------------
My Session Info:
R version 2.15.1 (2012-06-22)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF...0 zlibbioc_1.4.0
--
Sophie LAMARRE
Statistician - FRANCE
[[alternative HTML version deleted]]
</div
the Arabidopsis ath1121501
annotation package? The function GOHyperG requires a vector of
LocusLink identifiers, however LocusLink identifiers don't seem to be
available in the latest ath1121501 package since it is based...this limitation and use this annotation
package with GOHyperG?
I have tried to use alternative loci identifiers, but this resulted
in the below error message. Here is an examp…
updated 20.5 years ago • Thomas Girke
c("BP","CC", "MF")]
> gCmat <- matrix(as.integer(gCnums), dimnames=list(c("BP","CC","MF"),
"Number of terms"))
> xtable.matrix(gCmat, display=c("d","d"), caption="Number of GO
terms
per ontology.", label="ta:GOprops")
Error: could not...find function "xtable.matrix"
> xtable:::xtable.matrix(gCmat, display=c("d","d"), caption="Number of
GO
terms per ontology.", label="…
updated 16.3 years ago • Heidi Dvinge
div class="preformatted">Venu,
Thanks for your kind words and feedback!
Which version of ChIPpeakAnno did you use? This function has been
modified
extensively recently. Could you please try the new one...a wonderful tool for the
scientific
> community. I tried using chippeakanno software for identifying the
> distribution of enriched regions with "assignChromosomeRegion". The
o…
updated 12.7 years ago • Julie Zhu
biocLite("biomaRt")
ensembl = useMart("ensembl")
listDatasets(ensembl)
Once the dataset is identified, use the following example to select
the dataset.
hg = useDataset("hsapiens_gene_ensembl",mart=ensembl)
The getBM...learning Bioconductor.
Thanks,
Philip Terry
pterry@huskers.unl.edu
[[alternative HTML version deleted]]
</pterry@huskers.unl.edu></div
div class="preformatted">
Hello all,
I'm trying to use DEXSeq to identify and quantitate alternative
splicing events following transgene expression. I've used BWA to map
my reads and now...I used a perl script as a workaround."
Thanks in advance,
Wyatt
-- output of sessionInfo():
R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8…
homo+sapiens.xml',
reason 'Invalid argument'
Error: XML content does not seem to be XML, nor to identify a file
name 'query"Crohn's+Disease"homo+sapiens.xml'
I suspect that, because I am trying a multiple word keyword search...Is this actually the problem? Is there a work around this?
Thanks!
-- output of sessionInfo():
R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)
l…
updated 13.5 years ago • Guest User
5
Level 6
Level 7
Level 8
Level 9
Level 10
Level 11
Level 12
Level 13
Level 14
Level 15
Identified 37 main clusters in level 3 with MSS = 0.08025142
Running down without collapsing from Level 3
Level 4
Level 5
Error...can anyone point me in the right directions?
thanks in advance
Ivan
> sessionInfo()
Version 2.3.0 (2006-04-24)
i386-pc-mingw32
attached base packages:
[1] "m…
updated 19.5 years ago • Ivan Baxter
TRUE, show_rownames = FALSE,
cluster_cols = TRUE, annotation_col=inf)
sessionInfo( )
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6
```
This code runs fine and
updated 2.9 years ago • Josiah
<div class="preformatted">Dear list,
it looks like there may be a bug in function 'getBM' affecting the use
of
attribute 'validated':
----------------------------------------------------------------------
----------------------------------------------
>library(biomaRt)
>mart = useMart("ensembl")
>ensembl = useDataset("hsapiens_gene_ensembl", mart = mart);
>lib…
updated 16.7 years ago • Teresa Colombo
I wanted to use EnsDb.Hsapiens.v86 and org.Hs.eg.db combined, as both databases do not exactly display the same type of information (for example, only EnsDb.Hsapiens.v86 provides with biological function, or list of exons).
However, as you can see on below code, I was quite disappointed to notice that a great number of SYMBOL genes of org.Hs.eg.db weren't in EnsDb.Hsapiens.v86, and respective…
updated 4.9 years ago • bastien_chassagnol
n) : 'Calloc' could not allocate memory (1000000 of 16 bytes)
The information below is for the r version of my computer, which has 12 GB of RAM. platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32 systems...status
major 4
minor 1.0
year 2021
month 05
day 18
svn rev 80317
language R
version.string R version 4.1.0 (2021-05-18)
nickname Camp Pontanezen
memory.l…
updated 4.3 years ago • Yoan
describe count as:
"geneCounts
returns an "integer" vector: for each category term tested, the number
of
genes from the gene set that are annotated at the term."
> hypTest <- new("KEGGHyperGParams", geneIds = dGenes,
+ annotation...04020`
[1] "Calcium signaling pathway"
>kpath <- as.list(org.Mm.egPATH2EG)
# Remove pathway identifiers that do not map t…
updated 13.1 years ago • Mary Kindall
perform differential gene expression analysis. However, I
was wondering if it would be possible to identify cell type specific
marker genes for these cell types.
Genes that are predominantly expressed in a particular cell...all
combinations.
My question is to find out if there are any direct method that is
available to identify a set DEG's that explicitly belong a cell type
from a given dataset…
updated 12.7 years ago • Guest User
to find peaks that are significantly diferentially bound between the two groups of samples, and thus identify epigenetic differences between the two cell-types, using the 8 matched pairs of cell-type from the same individuals...They cluster nicely on the heatmap and on the PCA.
And there are 1594 differentially bound peaks identified with edgeR, using the default threshold of FDR <= 0.0…
I'm trying to use a quad gate to identify CD56++ (double positive) CD16+ cells. As such, I'm trying to force the quadrantGate function do find the separation point...major CD56 signal peak (the CD16 separation point is perfect). Unfortunately I can only get it to identify the separation point on the low side for CD56 which is not what what I want. Grateful for any suggestions.
```r
flowStats
updated 3.4 years ago • Christopher
The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly...pbcmc
GeneSelector
ampliQueso
prot2D
We will continue to identify packages that are not maintained/unresponsive to be deprecated in release 3.9
slightly from previous results that were generated at the end of August (with a presumably older version of DESeq2).
I am using a multifactor comparison, there are 24 samples with two states. In one example, a gene that was barely...NEWS" on the Bioconductor page) don't seem to contain Information on what changed between the last version in the file (1.13.8) and the current 1.14.0.
Is it maybe …
updated 9.1 years ago • Daniel Elsner
with this script:
===============================
library(AnnBuilder)
mypkg <- function(pkgPath, version) {
ABPkgBuilder(baseName="mybase.txt",
baseMapType="ll",
pkgName="mypkg",
pkgPath=pkgPath,
organism="Gallus gallus",
version...version,
author=list(
authors="Nian…
updated 19.3 years ago • Nianhua Li
of the knockdown only category.
However, whatever I enter for lfc in the decideTests function, the
numbers
of genes in the resulting diagram stay the same, whilst from manual
comparison of the data, they should not. Does anyone...fit, cont.matrix)
fit$genes=fData(BSData.filt)
ebFit=eBayes(fit)
veh=topTable(ebFit, coef=1, number=500)
cpt=topTable(ebFit, coef=2, number=500)
write.table(veh, file="d…
<div class="preformatted">Dear all
A very simple question question.
I'm analysing some HTS data withe 1536 plate and the library is made
by 17 plates.
I had the need to remove one plate from the analysis (plate 4).
When I tried to run the analysis again changing just the plateList
file, removing the rows releted to the three replicate of plate 4, I
got an error sayng:
Error in (function …
updated 11.3 years ago • Guest User
fail :in the doc it is
stated
" To run the function can be quite time consuming, depending on
the number of reads"
myreadpair<-reads2pairs(myread)
#drop single reads
myread<-myread[!(myread$ID %in% myreadpair$singleReads...sharing your experience in getting QC for large files
efficiently
Nathalie
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-…
<div class="preformatted">Hi,
probably a question for Rafael...
I get an error message with gcrma...and some warning messages...? What
can I
do with these ?
Thanks again
Philppe
R : Copyright 2003, The R Development Core Team
Version 1.7.1 (2003-06-16)
> library(gcrma)
Loading required package: affy
Welcome to Bioconductor
Vignettes contain introductory material. To view…
gt; length(c(rle, rle, rle))
[1] -1294967296
Probably, it is caused by the maximum positive number (~2.1E9) that
can
be represented by an integer variable. However, there is no warning
message.
I noticed this problem when...of length ~3*109, but mean() does not work on that vector.
Best,
Hans-Ulrich
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
l…
updated 14.0 years ago • Hans-Ulrich Klein
soapArgs =
list(org = org), :
data length [255] is not a sub-multiple or multiple of the number
of rows [128]
Thank you ,
Jenny
######################################
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=Greek_Greece.1253...1.1 SSOAP_0.8-0
stats4_2.15.1
[6] tools_2.15.1 XMLSchema_0.7-2
[[alternative HTML version delete…
design)
> dSplice <- diffSplice(fit[,"Dis1"], geneid="geneNames", exonid="start")
Total number of exons: 787188
Total number of genes: 31123
Number of genes with 1 exon: 4769
Mean number of exons in a gene: 25
Max number...gene with 504,965 exons?
Many thanks for any help/advice.
<pre>
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform:…
updated 8.6 years ago • willj
Should the transcript IDs in the BAM file and the annotation table match exactly, including version numbers (e.g., ENST00000335137.1 vs. ENST00000335137)?
Are there any preprocessing steps required for the GTF or FASTA
updated 9 months ago • ramya2kumar0
DiffBind allows you to plot PC1, PC2, and PC3 against each other but does not provide the actual numbers, nor does it provide access to any further PC's. Any help with this would be greatly appreciated.
dba.PCA documentation...https://www.rdocumentation.org/packages/DiffBind/versions/2.0.2/topics/dba.plotPCA
Thanks
updated 4.6 years ago • Spendlove
Recent ...
Replies
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43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
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Michael Love
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The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup.
Maybe give the traceb…
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For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
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