lt;-summary(sam.out,5.8)
>sum.sam.out
SAM Analysis for the Two-Class Paired Case
s0 = 0
Number of permutations: 100
MEAN number of falsely called variables is computed.
Delta: 5.8
cutlow: -7.086
cutup: 6.704
p0: 0.146...Identified Genes: 7988
Falsely Called Genes: 0
FDR: 0
Identified Genes (using Delta = 5.8):
Row d.value stdev rawp q.value R.fold
Order by: Relevance
Tiger) machine, I had trouble
building the latest RCurl and so the BioC extra repos is at older
version RCurl 0.95-1. If there is community demand for sorting out the
Mac OS X 10.4 (Tiger) issue, I'll look into finding out what...bioconductor at="" stat.math.ethz.ch="">
>> Subject: Re: [BioC] biomaRt - current devel version of
biomaRt+RCurl
>> don't work
>&am…
div class="preformatted">
Dear mailing list,
I am doing dual color hybridization using the last version of the
miRNA microarrays from exiqon ("7th generation").
Applying the limma package, data are background corrected...DupCor) and lmfit is performed.
I used the following script, which works fine at least until exiqon
version 11, since the 4 replicates are regularly distributed:
# identify …
of differentially expressed/spliced transcripts in my experiments. Using DEXSeq it is easy to identify the differentially used exons for each gene and by running
plotDEXSeq(dxr, "gene-name", displayTranscripts=T, names...T, legend=T)
it also possible to identify the transcripts for each gene.
Now, theoretically I would be able to identify which transcripts are present in which...for…
updated 10.6 years ago • peter_venhuizen
those redundant regions). Any help is much
appreciated!
Thank you,
CL
[[alternative HTML version deleted]]
</div
data (proteomic, expression) from a variety of
species (mouse, rat, pig, human) with lots of primary identifiers
(GI-number, ensembl gene ID, gene-symbol). What we need to do is take
such an identifier, say a mouse ensembl gene ID, and
updated 13.4 years ago • k. brand
an analysis of protein microarray data and have found that limma performs very well in terms of identifying positive controls in the assay. Unfortunately, there are a large number of known, non-specific interactors that...previous people have been identified in earlier experiments. For the pipeline I would like to down-weight, but not exclude, these proteins from the analysis
updated 7.3 years ago • andrew.birnberg
Hi all, I'm working with my RNA-Seq raw count data right now. I'm in the process of determining differentially expressed genes among the file, and I used DESeq2 package for R to do that.
\#run the DESeq pipeline
dds <- DESeq(dds)
\#delete all the data that have total of 0 counts
dds<-dds\[rowSums(counts(dds))>1,\]
\#get differential expression results
res<-…
updated 9.2 years ago • fromhj304
list,
We are running R-2.3.1/BioConductor on a Sun machine. I am wondering
how I
can check which version of BioConductor, 1.8 or 1.7 for example, was
installed? Do I need to check package(s) of my interest by
packageDescription...and see what version of R this package was built
with?
Thanks for your help in advance!
Jianping
##################################
Jianping Jin Ph.D.
Bioinformatic…
updated 19.3 years ago • Jianping Jin
question has been answered long time ago, but I have just
tested function justRMA() with different versions of package affy and
found the following behavior:
The results obtained with version affy_1.14.2 for BioC 2.0 and...earlier
versions are different from the results obtained with version
affy_1.16.0 for BioC 2.1 and later versions. Interestingly...affy_1.16.0
is the first version to use the …
updated 16.4 years ago • cstrato
class="preformatted">Hi all,
Just wonder if anyone knows how to export the results from LOH, copy
numbers, and major copy proportions (MCP) analyses from dChip?
I am new to the sofware and haven't found the functions for these
updated 17.2 years ago • Yu Chuan Tai
AA Kredit Loan CUSTOMER Care Helpline Number {{7008172090}}×8653694404+Toll free number contact me//7008172090=Call me
updated 2.6 years ago • Hena
I'm quite fresh in R and try to install "ggplot". my Rstodio's version is 3.2.0 but the point is my R version can't identify this package and had to upgrade my R! is there anybody who
updated 9.3 years ago • ghaffarian_77
genes between three contrasts and when I call the topTable function, many probesets with NULL/NA identifiers are returned (see below). I would like to filter all probesets containing N/A from the expression set object...data.fit,contrast.matrix)
data.fit.eb = eBayes(data.fit.con)
TT<-topTable(data.fit.eb,coef=1,number=Inf,adjust="BH",p.value=0.01,lfc=1.5)</pre>
<tab…
updated 9.0 years ago • mat149
Hi all,
I have been using the __Kallisto -> Sleuth__ pipeline on my RNAseq data consisting of a control and two treatments (in triplicates). From that I got 8 DETs (q-value < 0.05) for treatment 1 and 12 DETs for treatment 2. The highest beta (_"equivalent"_ to log fold change) were around 6 and the lowest -4.
In order to validate my results from Sleuth,…
wondering whether there is a method in limma which allows you to do an ANOVA like test which will identify any differences between treatment groups, instead of doing multiple pairwise comparisons? I would also
updated 9.6 years ago • brionyk9
I'd like to know whether the version of a database used in a given Bioconductor package will always be the same, given the same version of Bioconductor...In other words, is the version of Bioconductor synonymous with a given version of a database that a package is based upon?
For example:
Will Bioconductor...per GO.db manual)?
*Or* is there a possibility that the GO.db package will reference …
updated 3.9 years ago • rebeliscu
Hi all,
I have a general question about the model estimation used by DESeq. There have been many posts on whether or not DESeq works well with a small number/no replicates, but I'm wondering if it's appropriate to use DESeq for differential analysis across two conditions, where...used by DESeq. There have been many posts on whether or not DESeq works well with a small number/…
updated 8.2 years ago • krc3004
time to fix the batch issue in cellHTS2. Things
should work fine now in both the updated release version (2.10.1) and
the
latest devel version (2.11.1)
Thanks again for the notice and let me know if you encounter other
problems...general explanation of variance adjustment, what it does and why?
Additionally, when I add the batch number to the plate list and ask
the
program to do a variance adjust…
updated 16.1 years ago • florian.hahne@novartis.com
could I modify the clustering parameters ("the resolution") in order to increase/or to decrease the number of CLUSTERS ?
thanks a lot,
- bogdan
div class="preformatted">What package would I need to transform Genbank accession numbers into
gene symbols or entrez gene ids? e.g.If I search "R28020" on NCBI, it
tells
me that "This EST is one of 1366 sequences...Is there a metadata package that has this kind of information in it? I
have a
couple hundred such identifiers that I need to map to genes. I'd like
to
be able to run
getSYMBOL("…
updated 12.2 years ago • Ed Siefker
Hello Bioconductor,
I'm working on RNA and small RNA seq and I'm a bit confused
regarding the version that I can use between the alignment of fastqs
and R packages.
The trouble starts when I try to make my own GTF file for...small RNA sequences that
exist in other databases and I don't want to mix up sequences from one version, genomic ranges from another and transcripts from another one.
I mak…
updated 4.9 years ago • Konstantinos Yeles
div class="preformatted">Hi,
I'm trying to compute the copy number for the Illumina 660W-Quad bead
array
with the package crlmm. But for some chromosome it doesn't work and I
get the
following...samples in the CrlmmSetList object were
processed together in the same batch.
Fitting model for copy number estimation...
Using 50 df for inverse chi squares.
Sufficient statistics
.
Estimating coeffic…
<div class="preformatted">Dear all,
Version 2.1.0 of the globaltest package is now available. Globaltest
tests
whether the expression profile of a geneset/pathway...div class="preformatted">Dear all,
Version 2.1.0 of the globaltest package is now available. Globaltest
tests
whether the expression profile of a geneset...is associated with
a
clinical variable.
Main new features of versi…
updated 21.7 years ago • Goeman, J.J. MSTAT
Hello,
Running:
<pre>
docker run -ti bioconductor/release_core:20160630 R</pre>
I get:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
...
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning message...BiocInstaller version 3.2 is too old for R version 3.3.1; see
https://bioconductor.org/install/\#troubleshoot-biocinstaller
 …
updated 9.4 years ago • Karl Forner
Hello,
Me and a colleague are performing differential expression analysis on a dataset comprised of 2 groups, controls and cases. We wanted to test/correct for batch effect so we decided to use SVA and we were obtaining the initial files from a shared folder.
We were however getting different results. We thought it might be due to small differences in our scripts, however, w…
updated 8.5 years ago • dmffrancisco91
Hallo everybody!
I am trying to install Agi4x44PreProcess on a Windows-mashine using R version 3.1.2 and Bioconductor version 3.0 (BiocInstaller 1.16.1).
As I understand Agi4x44 depends on R (>= 2.10), yet I am unable...to install it.
Error message reads: "package ‘Agi4x44PreProcess’ is not available (for R version 3.1.2)"
Is there a work-around known to implement the functions of th…
updated 11.0 years ago • dimitri.leonid.lindenwald
and they appeared different commands compared to the ones on the tutorial. I then looked at the versions and when I install using biocLite, it appears to be downloading version 1.2.0 instead of 1.4.1 as mentioned on the...bioconductor page. Can this be updated please? Please see sessionInfo()
<pre>
R version 3.4.0 (2017-04-21)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Ce…
events and I have many samples, so the calculation takes a long time. Is there a way to reduce the number of events? A way to take a good representative sample, and then run my GatingSet on them?
Thanks
updated 3.9 years ago • markkelly1983
div class="preformatted">TarBase identifies gene-targets through three identifiers, namely
"HGNC_ID", "HGNC_Symbol", ENSGxxxxxxxxx",
Which one of such identifiers...of assigning them ... but I am
missing their usage and difference with other
*to my eyes* similar identifiers.
TarBase contains 1 miRNA called "Edited-miR-376a-5p". Could you please
explain the meaning of this name and advice...a…
analysis of control and treated samples. However, I am not sure if DEseq takes into account number of initial reads in fastq files or number of aligned reads after salmon. Because I assume the greater the percentage
updated 7.0 years ago • danalvoronov
<div class="preformatted">Dear all,
Using aroma.affymetrix I have fitted a GLAD model and would like to
extract
the (relative) copy-numbers.
Following the aroma-affymetrix website I did:
# get cdf
> chiptypes <- c("Mapping250K_Sty", "Mapping250K_Nsp")
> cdf <...Using aroma.affymetrix I have fitted a GLAD model and would like to
extract
the (relative) copy-number…
updated 17.8 years ago • Christian.Stratowa@vie.boehringer-ingel…
with the numeric
value.
In other words, how can I plot and annotate the edge of the network
in
numbers? Please see the example below:
0.573
nodeA <-------------->nodeB
Thank you for the kind response.
Shih-Te
------------------------------------------------
Shih-Te Yang, Ph.D. student
as far as I’m aware, those gene sets are only available as HGNC gene symbols (e.g., IDS) or Entrez identifiers. My RNA-Seq reads were mapped to ensembl gene identifiers (e.g., ENSG00000010404). I tried converting my ensembl...were no duplicated ensembl identifiers to begin with). Additionally, some ensembl identifiers could not be mapped to HGNC symbols. I ended up leaving the...duplicated HGNC s…
updated 6.0 years ago • Jeremy Beales
div class="preformatted">Hi all,
I made the fatal mistake of updating affy after the devel version
started requiring R >= 1.8.0 and before it actually became compatible
with 1.8, so I am stuck in no-man's land (I realize...I can use the
release version, but I like some of the functionality of the devel
version better).
Is there some magical place on the bioconductor website...that I h…
updated 22.2 years ago • James W. MacDonald
I used R version (2.5.0) . I want to install GO.db but it gives error like
<pre>
> source("http://bioconductor.org/getBioC.R")
Error in value...inherits) : variable ".BioC_version_associated_with_R_version" was not found</pre>
If i install R version(2.7.0) and install GO.db. I gives error after loading the GO.db
<pre>
library(GO.db)
Error:
>Loading required…
of one ATAC-Seq data. When I don't trim any reads, it seems that our library complexity (cell number) is not enough because of a saturation plateau (fig. 1). However, it appears that the library complexity (cell number) is enough...2). I don't know which one is correct. Could you help me? May I know how ATACseqQC estimates the number of putative sequenced fragments and distinct fragments beyond t…
updated 6.7 years ago • Gary
<div class="preformatted">zhijin, Jim and Saroj:
After trimmed those extra probe from probesequece file, I finally make
gcrma start to work.
Thank you very much for your great help.
When I got those updated cdf and probesequence file, I checked and
confirmed that all of probeset ID show in cdf file also show in
probesequence file. But I did not check reversely. Saroj help me
identify
that…
preformatted">Dear all,
Is there an annotation function in BioConductor to map "Gene Accession
Numbers" from a Rosetta chip to GO terms and vice versa?
Here's 10 gene accession numbers as an example:
[1,] "Contig9452_RC"
[2,] "NM_003088
updated 21.6 years ago • Goeman, J.J. MSTAT
Where to find the repository for DESeq2 old version, for manual installation
div class="preformatted">Hello,
I've tried to install the latest stable version of Limma.
With "biocLite()" command I get Limma 2.9.8 but if I use the
"install.package" command I get Limma 2.8.1.
How can...I get the latest "stable" version of Limma package?
With the following commands I get Limma 2.9.8 (Is it a stable
version?)
source("http://bioconductor.org...command I get Limma 2.8.1
…
Loft Money Loan Customer Care Helpline Number☎️7980441001__8116494943Loft Money Loan Customer Care Helpline Number☎️7980441001__8116494943
updated 2.6 years ago • mapadad821
Loft Money Loan Customer Care Helpline Number☎️7980441001__8116494943Loft Money Loan Customer Care Helpline Number☎️7980441001__8116494943
updated 2.6 years ago • relodoy154
Loft Money Loan Customer Care Helpline Number☎️7980441001__8116494943
Loft Money Loan Customer Care Helpline Number☎️7980441001__8116494943
updated 2.6 years ago • dasima7714
In order to install the cellnetr package, I need the affy package version 1.36.1.
The current version is 1.48 (http://bioconductor.org/packages/release/bioc/html/affy.html)
Is there a way to...find previous versions of this package?
Thank you
updated 9.8 years ago • burton.mendonca
I keep on getting this warning message when I try to install cytofkit in R version 3.6.3.
```
> BiocManager::install("cytofkit")
Bioconductor version 3.9 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing...nlme, nnet
Old packages: 'fs', 'plyr'
Update all/some/none? [a/s/n]:
a
There are binary versions available but the source versions are later:
binary source ne…
updated 5.8 years ago • Mari
GenomiFeatures I get this error:</span>
BioC\_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.1.
Installing package(s) ‘GenomiFeatures’
Warning message:
package ‘GenomiFeatures...is not available (for R version 3.2.1)
\# R session:
<span style="line-height:1.6">> sessionInfo()</span>
R version …
updated 10.2 years ago • serpalma.v
messagings below.
"Warning in install.packages :
package ‘Rsamtools’ is not available (for R version 4.0.2)".
This R version is the latest version. Is there anything else we can do?
Thank you very much for the help
updated 5.4 years ago • yusuke_suita
Hi,
I am trying to parse a BAM file using readAligned. It gives me an error of incorrect number of reads. How can I resolve this error. My command is as follows. The BAM file was generated by aligning to reference fasta
updated 7.0 years ago • kspata
the data, I found that swappedDrops crashed. I am wondering if there is a limitation to the number of cells swappedDrops can handle. Your inputs/insights will be much appreciated. Thank you.
Best,
Joon
updated 6.6 years ago • joseph.joonsang
nbsp;impute Ct values for the non-detects I have obtained on my RT-qPCR results. Is there a minimum number of genes I should have in my qPCR to provide enough data so than this R package is able to replace non-detects with
updated 8.3 years ago • garciaii_antuerpia
How is the minFDR value calculated for each cluster of CpG probes that are identified when running DMRcate on EPIC BeadChip data? I have a large number of differentially methylated positions (DMPs
updated 3.6 years ago • dgrayson
I'm interested in looking for recurrent somatic copy number aberrations (RCNAs) amongst the CNVs detected by CopywriteR using GISTIC 2.0 (which is arguably the standard tool...I'm interested in looking for recurrent somatic copy number aberrations (RCNAs) amongst the CNVs detected by CopywriteR using GISTIC 2.0 (which is arguably the standard tool used...for identifying RCNAs). As per the GISTIC …
updated 9.8 years ago • jcarter
I am currently using Aroma's ASCRMAv2 & Paired PSCBS to do a copy number analysis on Affymetrix GenomeWide SNP Array 6.0 data. I've run the data through but haven't yet seen a measure of...etc) created and stored in Aroma processing that I can use. If not, what do others use to identify bad samples?
Thanks in advance for any help,
Gaius
updated 9.5 years ago • gaiusjaugustus
Homo_sapiens.GRCh38.98.chr.DEXSeq.gtf ... ||
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
The specified gene identifier attribute is 'gene_id'
An example
updated 6.0 years ago • seung.ho.steven.choi
function has parameter `source = c("COSMIC", "SIGNAL", "SPARSE")`. COSMIC signatures are versioned. It would be good to have another parameter allowing the user fo choose the version (e.g. version 2). This could be useful
updated 4.5 years ago • Dario Strbenac
0.8.0" is not TRUE
> txi
Error: object 'txi' not found</pre>
I did, in fact, use a salmon version <= 0.8.0 (0.7.2 to be precise) as it was the most recent version available on my institution's HPC. Is there a work around...or alternative package/ function to use for the lower version? Or does some additional functionality exist in salmon version 0.8.0 and higher that is req…
I am a master student, I am new to the field and I have many difficulties.
I am currently trying to identify the most methylated sites of tumor samples and normal TCGA-GBM tissue.
However, when I use the get.diff.meth function
<div class="preformatted">Seth Falcon wrote:
> Hi Jim,
>
> Any insight on this one?
>
> "Na, Ren" <na at="" uthscsa.edu=""> writes:
>
>>Hi, I tried to find the genes in some of significant GO categories,
>>and find out Counts of EntrezIDs returned from summary() are not
>>same as the numbers of entrezI…
updated 18.6 years ago • James W. MacDonald
<div class="preformatted">Dear List,
I have another question with the xps package. I installed root and
xps, created the root schemes for the HuGene1.0 array and imported the
first CEL files following the example scripts. Everything works fine
to that point. However, after RMA normalization I'm missing a couple
of probesets. When I use the Affymetrix expression console you get
33297 probes…
updated 16.5 years ago • Michael Walter
Recent ...
Replies
Comment: GOseq Probability Weight Function bad fit
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ejasge.r.m
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When performing GO analysis with GOseq, i s important to carefully check your input and assumptions, just like reviewing choices on the McD…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★
5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
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efoss
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I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
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53k
Answered here: https://support.bioconductor.org/p/16318/
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