div class="preformatted">Lukas (and others):
I'm using the new version of MEDIPS (1.10.0) and I'm getting an error
when trying to use MEDIPS.createSet():
MEDIPS.createSet(file="myalnment.bam...0, uniq=T,
window_size=100)
Here's the error I get:
Reading bam alignment myalnment.bam
Total number of imported short reads: 6150717
Extending reads...
Error in regions$stop[regions$strand == "+"] =…
Order by: Relevance
<div class="preformatted">Hello,
I am pretty new to marray and actually having the same problem.
When using read.GenePix() I get the error
""Error in if (skip > 0) readLines(file, skip) :
> missing value where TRUE/FALSE needed"
Additionally I get a warning message
": In grep(layout.id[1], y) :
Inputstring 30 not valid with this locale."
When using the skip optio…
Is it possible to keep sequence names when haplotypes are collapsed using the Collapse tool of the QSutils package?
I have a number of fasta formatted sequences, some of which are the same, and therefore redundant for a phylogenetic analysis; since I would like to remove those that are already represented, I am using the Collapse function of QSutils to remove them. My issue is that after using…
updated 5.9 years ago • al.gar.aber
Hi, I am using biomaRt to retrieve gene annotation using Ensembl IDs, and the exact same code that worked properly just a month ago, now throws errors.
Please check the MWE below:
<pre>
library(biomaRt)
ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="www.ensembl.org")
genes <- c("ENSG00000121671", "ENSG00000142208", "ENSG000001…
updated 8.5 years ago • daniel.carbajo
TilingHuman10R01 3104980
TilingHuman10R01_Hs_ENTREZG
That means tiling chip number 1 is mapped to custom CDF
TilingHuman10R01_Hs_ENTREZG.
So for the tiling arrays celfiles you have, I think you can...them by chip number first, then for each chip number, you
only need to do ReadAffy and analysis once.
Tiling array custom CDF probe package...mm probe, which is also …
16.7 . .
GT:PL:GQ 0/0:0,3,38:5 0/0:0,0,0:3 0/0:0,6,63:8
0/1:54,6,0:4
</id=pl,number=g,type=integer,description="list></id=sp,number=1,type=integer,description="phred-scaled></id=dp,number=1,type=integer,description...phred></id=pchi2,number=1,type=float,description="posterior></id=pc2,number=2,type=integer,description="phred></id=indel,numbe…
in
my set of genes, the gene attached to it is also represented.
I would have expected to find the numbers -- genes having a specific
GO
term in my list being "1" and genes having the term in total, in the
annotation, being "1" as well...13
and
62 genes are denoted. Please have a look at my script and the session
info:
SessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-redhat-linux-g…
updated 11.7 years ago • Christine Gläßer
The devel version of gwascat (2.1.15, see <http://bioconductor.org/packages/devel/bioc/html/gwascat.html>) includes a number of new features
updated 10.4 years ago • Vincent J. Carey, Jr.
1] the reviewer has pointed out that the Licence
tag in the description file does not contain any version number.
I assumed it was meant to be "GPL v2 or later". In order to confirm it
I
have emailed twice Mr Li (on February 16 and
5' most base, whose position was shifted. For example, the 5' most base is first shifted by a fixed number based on POS and CIGAR fields, then reads are summarized. It is useful if the middle point of fragments are considered...only in plus or minus strand of the genomes?
I also expect these options can be added in the linux version.
Thanks
updated 7.3 years ago • Leon
<div class="preformatted">I would like to use some of the simple annotation aspects of
Bioconductor
but have had difficulty building a full package (another question for
another day). However, I would like to be able to use, for example,
alongchromosome from geneplotter without having to explicitly build a
data
package. I can fairly easily make an environment that contains (for
this
examp…
updated 22.2 years ago • Sean Davis
function that I am using is the intronsByTranscript(). While this
function is useful, it returns the number of raw reads that align to
each
intron grouped at the transcript level. Is there an easy way to get it
to
group it by a gene...that we use the intronsByTranscript()
function.
Thanks,
Fong
[[alternative HTML version deleted]]
</div
updated 12.9 years ago • Fong Chun Chan
raw.data
AffyBatch object
size of arrays=1164x1164 features (32 kb)
cdf=HG-U133_Plus_2 (??? affyids)
number of samples=35
Error: package 'hgu133plus2cdf' was built before R 3.0.0: please re-
install
it
In addition: Warning message...Thanks and Regards:
Farahdeeba Shaikh
Msc-Bioinformatics
[[alternative HTML version deleted]]
</div
test.intensity=pm(test)
test.intensity is a matrix with rownames of qualifier#, where # is a
probe
number. For example, mygene1, where mygene is the qualifier and 1 is
the
first probe for that probe set with qualifier "mygene...510-428-8546(Emeryville)
*****************************
[[alternate HTML version deleted]]</div
div class="preformatted">Hello,
There seems to be a problem with read.ilmn() with the new version of
limma. When trying to read the control file, there is an error that
row names are not unique.
x <- read.ilmn(files="probe...2600040?,
?6450180?
I looked at the control file, and there are indeed 3 rows with the
same ProbeID number. I?m not sure if that is an error or something
about…
updated 11.9 years ago • Scott Christley
I am trying to annotate a [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] file in affylmGUI. I downloaded the
> if (!requireNamespace("BiocManager", quietly = TRUE))
+ install.packages("BiocManager...RenderBadPicture (invalid Picture parameter)
2: package ‘hugene10stv1.db’ is not available (for R version 4.0.2)
3: package ‘hugene10stv1.db’ is not…
updated 5.2 years ago • kiera.lee
tr>
<tr>
<td>HMSC_tot</td>
<td>mesenchymal_stem_cells</td>
</tr>
</tbody>
</table>
I have different number of samples per group ( I don't know if it could have an influence , 2samples for mant, 3 for late\_treated, 1 for mesenchymal
updated 9.1 years ago • ZheFrench
generate a theoretical translatome. This protein database was then used to search mass spec data to identify proteins in my samples. I next mapped the identified proteins back to their transcript IDs and sequences and was...to see them)
```
The code seems to have worked for the first few entires. Here is the truncated version for the entries that worked:
header | 1 | 2 | 3 |
--------- |…
updated 4.0 years ago • nattzy94
<div class="preformatted">Dear jial2,
As others have pointed out, a sample should only be removed as an
outlier
if it is quite clear cut, preferably with some identifiable cause.
It is however possible to allow for some samples being less reliable
than
others, and it is usually preferable to do this in a graduated way
rather
than complete removal. In my lab, we regularly use the arrayWei…
updated 12.3 years ago • Gordon Smyth
allowed
Error in getBM(c(att, "gene_biotype"), filter = "ensembl_gene_id",
value
= "ENSG00000187634", :
Number of columns in the query result doesn't equal number of
attributes in query. This is probably an internal error, please...Attribute biotype NOT
FOUND
Error in getBM(c(att, "structure_biotype"), filter =
"ensembl_gene_id", :
Number of columns in the query result doesn't equal numb…
start_position", :
The query to the BioMart webservice returned an invalid result: the
number of columns in the result table does not equal the number of
attributes in the query. Please report this to the mailing...list.
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF...4
>…
must be a numeric
vector
of length 1 with values between 0 and 2400.
> sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32
locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETAR...AffyBatch object
size of arrays=100x100 features (27 kb)
cdf=cdfenv.example (150 affyids)
number of samples=3
number of genes=150
annotation=
notes=
##############################…
updated 17.5 years ago • Markus Schmidberger
gt;>>>>>>>> Just comparing two batches (TB1 and TB2) with
different probe numbers:
>> >
>> > >>>>>>>>>>> length(TB1$genes)
>> >
>> > >>>>>>&…
updated 14.6 years ago • Gavin Koh
flow cytometry dataset which I now want to analyze computationally. My aims are two: I first want to identify subpopulations that are not easily seen in 2D-plots of usual markers and second, I want to see whether the identified...populations between two conditions. From the paper and the vignette, I understand that *cydar* can identify these subpopulation and I wanted to ask how one would present…
updated 5.7 years ago • tkapell
hello, I'm working with some RNA seq data from a clinical trial. There are about 160 patients (40/group with low, medium, high doses of a drug plus a placebo group). Samples were taken at baseline, week 4, and week 12. I would like to identify genes that are differentially expressed by the drug vs placebo and to explore if there is some sort of dose response in gene expression. Can someone offer …
updated 10.5 years ago • rvinisko
additive, yielding a net
effect on C that is increased by 3-fold compared to baseline. We wish
to identify, visualize and study these scenarios within KEGG annotated
pathways.
I expect that this sort of analysis is implemented...Gregg Lab Website: www.neuro.utah.edu/labs/gregg/index.html
[[alternative HTML version deleted]]
</div
<div class="preformatted">Hi January,
2011/2/28 January Weiner <january.weiner@mpiib-berlin.mpg.de>
> Dear all,
>
> my tool of choice currently is SPIA, a package that seems to provide
> sophisticated analysis of pathways (including both, gene set
> enrichment analysis and pathway perturbation analysis). I wonder
what
> other tools you could…
Hi,
I have been working with Diffbind to identify differential binding of H3K9me3 due to ethanol treatment. We are using both males and females, and initially ran...appropriate to use for normalizing factors such as tissue type or batch? Or could this be used to identify differentially bound regions between two main factors?
Thanks for your help
updated 21 months ago • erbrocato
<div class="preformatted">Hi,
I am not having any prior experience in using R/Biocunductor
software, can any one please help me in writing a function that takes
a list of entrez gene identifiers as an input (e.g. differentially
expressed genes in a gene expression study) and a list of background
genes (e.g. entrez gene identifiers of all probed genes on the
microarray) and performs a hyp…
disease group:"
> lrt <- glmLRT(fit, coef=10:12)
> topTags(lrt)
I'm interested in identifying the genes that respond to hormone in __all__ disease groups. How is the glm constructed to identify genes that
updated 10.6 years ago • joanna.l.kelley
In scan(file, what, nmax, sep, dec,
quote,
skip, nlines, na.strings, :
number of items read is not a multiple of
the
number of columns
All suggestions are really appreciated!!
Hui-Yi
[[alternative...HTML version deleted]]
</div
updated 17.1 years ago • Hui-Yi Chu
<div class="preformatted">
Hi,
I am new user of edgeR for gene expression analysis. I am testing
three different condition, and with pairwise comparison between them I
have been able to get the DGE genes for each comparison.
I have two questions:
1) I ran the DGE analysis with and without the low count reads filter.
When I did not use a filter, I obtained thousand of DGE genes and I
could …
biocLite("ath1121501.db")
library("ath1121501.db")
genenames <- org.At.tairGENENAME[ids]
number<-org.At.tairENTREZID[ids]
xx<-toTable(entrez)
yy<-toTable(number)
complete<-merge(xx,yy)
I get an error in this step...and
their corresponding TAIR ID and TAIR genename and annotation.
-- output of sessionInfo():
R version 2.15
Linux.
--
Sent via the guest posti…
updated 13.1 years ago • Guest User
div class="preformatted">Hi all,
I am trying to analyze my array CGH data for copy number alteration
states with CGHcall. My code is as follows:
data.CGHcall <-
read.table("aCGH_18_log2ratio.txt",header...started ...
Errore in data.frame(regions2, genord = 1:nreg2) :
arguments imply differing number of rows: 0, 2
What kind of error could this be ? Could it be because of some pro…
is between uncomplicated
vs.
complicated i.e., CY3/CY5, but I also want to know what is the copy
number
variation in CY3 labeled sample and cy5 labeled sample individually
because both of them are disease conditions...for only single
array, and please let me know is there any way to find out how many
fold
the copy number variation is taking place
Regards
Isha Pandey
Email- isha.pandey@bits-pi…
updated 12.2 years ago • Isha Pandey Phd Scholar BITS Pilani Cam…
<div class="preformatted">Dear all,
sorry if this question is not appropriate to this list, but if you are
using DEXSeq probably you used htseq to make exon count previously.
While
making the counts using the python script available we saw that counts
are
being attributted to regions overlaping 2 genes, that what we think it
means the counts corrseponding to IDs that have 2 or more ensembl…
object where I set fold=1 and th=0.01
When I load these into an R session with the most up-to-date versions of packages, I see this message:
```r
Warning: Loading DBA object from a previous version -- updating...
```
and recreating the
updated 2.6 years ago • jandrade
AA868688"
This means that there is no entry for AA868688.
> This happens with all the GenBank identifiers that I am trying to
convert to
> Entrez Gene IDs. What am I doing wrong?
You are not doing anything wrong. NCBI supplies...genbank accession
numbers for what are essentially full-length transcripts that are
associated with a gene. However, if you look up the accession...gt;…
updated 17.5 years ago • Sean Davis
div class="preformatted">Using a recent version of R, I get an error running gcrma on hthgu133a
(high throughput Affymetrix U133A) chips. The error is
Error in pms[, i] <...GSB.adj(Yin = pms[, i], subset =
index.affinities, :
number of items to replace is not a multiple of replacement length
Calls: gcrma -> bg.adjust.gcrma -> gcrma.engine
Execution...eset,f…
<div class="preformatted">
Dear List,
I am working with some "Affymetrix GeneChip miRNA v1.0" chip data and
am recieving an error upon executing the gcrma method. Is this error
to do with the NSB estimation by any chance? If so is my only solution
to use simply rma instead?
Thanks,
Scott
> celFiles <- read.affy()
> celFiles
trying URL 'http://bioconductor.org/packag…
5 (NEUT.methSegs.bed)
2: In scan(file, what, nmax, sep, dec, quote, skip, nlines,
na.strings, :
number of items read is not a multiple of the number of columns
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-unknown...1173.full.pdf="" 31="" 9="" cancerres.aacrjournals.org="" content="">
[[alternative HTML version deleted]]
</http:></div
updated 12.9 years ago • Tim Triche
following error.
> x.contrast.REG <- topTable(fit.contrast, adjust.method="none",
coef=c(1:4), number=20000, p.value = 0.05)
Error in `row.names<-.data.frame`(`*tmp*`, value = value) :
duplicate 'row.names' are not allowed
In addition...I really hope someone can help me understand.
Regards,
Christian De Santis
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform:…
updated 12.1 years ago • Christian De Santis
start", :
The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing...list.
Here is the output of the session Info (biomaRt 2.26.1)
<pre>
R version 3.2.4 (2016-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows…
updated 9.7 years ago • lexitownley33
in some genes. The original data were analyzed a couple of years ago with DEXSeq (I ignore which version was used as the analysis was done by a previous colleague). To integrate the information about exon usage with infomration...about differential isoform expression I run BitSeq and Cuffdidd as comparison. While the number and the pattern of differentially expressed isoforms are quite consistent…
updated 10.5 years ago • elle
preformatted">Dear bioconductor list,
The mouse4302.db annotation package is listed as Version 2.02
of the
annotation
for mouse 4302 and was packaged Mon Oct 22 10:15:57.
The mouse4302 annotation package is listed...as Version 2.01 and
was
packaged
Thu Oct 11 11:31:47 2007.
Should I there use mouse4302.db as the more recent and
authoritative...I am wondering
why mo…
updated 17.7 years ago • Richard Friedman
<div class="preformatted">The problem would appear to be in your data object, about which you
give us
no information.
1. There has been work on write.fit() recently. Try updating to the
latest
version from CRAN and see if the problem goes away.
2. In the latest versions of limma, you can also try
write.table(fullfit, ...)
3. The problem is most likely that there is no component 'genes' i…
Analysis of
Microarrays
(SAM) that I have posted three days ago. I highly recommend to use
this new
version since I have fixed a few bugs and added to new features to
this package:
1. Now an one class analysis is possible (in the...previous version only
two
class analyses were possible).
2. I have added a new function called sam.lambda. If a previous
analysis
with...the function sam was assigne…
updated 22.5 years ago • Holger Schwender
gt; raw
AffyBatch object
size of arrays=602x602 features (53806 kb)
cdf=RAE230A (15923 affyids)
number of samples=19
number of genes=15923
annotation=rae230a
> show(raw)
AffyBatch object
size of arrays=602x602 features...53806 kb)
cdf=RAE230A (15923 affyids)
number of samples=19
number of genes=15923
annotation=rae230a
> sessionInfo()
Version 2.3.1 Patched (2006-08-06 r38829)
i3…
Hi all,
It's my first-time to analysis Affymetrix HTA 2.0 arrays \[transcript (gene) version\], data source <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi>. As a rookie, I have been bothered by its annotation
updated 7.2 years ago • Biomed
gt; raw.data
AffyBatch object
size of arrays=732x732 features (50240 kb)
cdf=Canine (23913 affyids)
number of samples=12
number of genes=23913
annotation=canine
> rma.data
Expression Set (exprSet) with
23913 genes
12 samples...object with 1 variables and 12 cases
varLabels
sample: arbitrary numbering
> sessionInfo()
R version 2.2.1, 2…
I apologize if this email shows up twice to the mailing list.
I'm trying to use ChIPpeakAnno to identify the annotation of ChIP-Seq
peaks
for an organism that does not have an annotation package. I have used
makeTranscriptDbFromGFF...AnnotationData = ep, :
AnnotationData needs to be RangedData object
sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
loc…
updated 12.4 years ago • Alan Smith
columns with character and double
values, as in following example:
? ? ? ?V1 ? ? ?V2 ? ? ?V3
identifier ? ? ?8.82427663558682 ? ? ? ?8.3543072605016
8.43568898178512
when I use:
> my_tab <- read.table(infile, header=TRUE...sep="\t",quote="")
numeric values are cut after 6th decimal place
identifier ? ? ?8.824277 ? ? 8.354307 ? ? 8.435689
thanks in advance
?stefan
</div
updated 15.4 years ago • Stefan Kroeger
exact covariance matrices. (This is not
quite
as simple as you might think, because lmFit supports a number of
different
covariance structures, robust fits etc, so the changes have to be made
in
a number of low level functions...the statement when a colleague in
> biology asked me why one would get different sets of probes
identified
> as differentially expressed, depending on which…
updated 15 days ago • Gordon Smyth
Attribute 3utr_start
NOT FOUND
Error in getBM(attributes = c("ensembl_gene_id",
"sequence_3utr_start", :
Number of columns in the query result doesn't equal number of
attributes in query. This is probably an internal error, please...report.
Presumably some transcripts have more than 1 3'UTR (hence the number
of columns difference described above)
Can anyone suggest a solution? Either a way …
I am interesting in identifying upstream regulators of a filtered group of transcripts, identified using either microarray or RNAseq technology...directions.
I have also used a Cytoscape plug-in called [iRegulon](http://iregulon.aertslab.org) to identify putative upstream regulators of groups of transcripts. I know that you can interface Cytoscape with R but was wondering
updated 7.2 years ago • lm795
chunk fails without an error.
###################################################
### code chunk number 15: layTrack (eval = FALSE)
###################################################
## track(session, "targets") <- targetTrack
# We know the code is failing due to the below code and output...table(trackNames(session)=="targets")
FALSE
223
R version 2.15.1 (2012-06-22)
Platform: i386-…
Running under zsh:
source getBioC.R [ 7:56]
getBioC.R:55: number expected
getBioC.R:62: no such file or directory: -
getBioC.R:69: bad pattern: writeLines(paste(Running getBioC version...If you encounter
problems,
first make sure that\n,\n you are running the
latest
version of getBioC()\n,\n which can be found at:
…
updated 22.5 years ago • Bela Tiwari
div class="preformatted">
Dear Raquel,
Thanks for the report. The current pint version has been designed for
and
tested with aCGH probe-level data. The framework should be applicable
to
segmented data...tries to avoid such information loss. Segmentation might help to
avoid overfitting when sample size (number of arrays) is particularly
small (compared to the number of probes within the region…
updated 15.6 years ago • Leo Lahti
answer is yes. Please see following:
>>
>>
>> mac$ R --vanilla
>>
>> R version 2.15.0 (2012-03-30)
>> Copyright (C) 2012 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>> Platform...to-Internal-
identical-which-requires-6-td4548460.html
>
>
> and t…
Hello !
I have a deseq object (called 'dds' here)
```r
dds
class: DESeqDataSet
dim: 11060 198
metadata(1): version
assays(6): counts avgTxLength ... H cooks
rownames(11060): FBgn0000003 FBgn0000008 ... FBgn0288846 FBgn0288856
rowData names(66): baseMean baseVar ... deviance maxCooks
colnames(198): 1 2 ... 1291 1425
colData names(10): library sample ... condition
```
the 'rownames' being FlyB…
updated 6 months ago • caroline.zanchi
Recent ...
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