correction : pmonly
expression values: medianpolish
background correcting...Error: cannot allocate vector of size 83200 Kb
In addition: Warning message:
Reached total allocation of 1024Mb: see help(memory.size)
Is this saying...that the vector size for each chip is 83Mb? Otherwise,
what is going on?
In addition, is this a reasonable analysis or is this duplicating
Order by: Relevance
applied to an object of class "c('DESeqDataSet', 'RangedSummarizedExperiment', 'SummarizedExperiment', 'Vector', 'Annotated', 'vector_OR_Vector')"
This even occurs when I run the example from https://www.rdocumentation.org/packages...applied to an object of class "c('DESeqDataSet', 'RangedSummarizedExperiment', 'SummarizedExperiment', 'Vector', 'Annotated', 'vector_OR_Vector')"
Does anyone …
Hi all,
I'm attempting to reproduce this [WGCNA output](https://www.dropbox.com/s/8yos9n4ct3vt2tz/WGCNA_figure.pdf?dl=0) with small cell lung cancer (SCLC) microarray gene expression data available from the [CCLE](http://www.broadinstitute.org/ccle/home). After importing gene expression data data, collapsing on genes, selecting the 8,000 most variable genes based on median abso…
updated 9.9 years ago • krr
I'm getting an error stating:
<pre>
barplot(gsea_BP)
Error in barplot.default(gsea_BP) : 'height' must be a vector or a matrix</pre>
or..
<pre>
dotplot(gsea_BP)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method
updated 5.2 years ago • tcalvo
pairs
counts <- do.call(cbind,lapply(gi.counts,function(x){
## Initialize a vector of counts 0 of the lenght of all interaction
counts <- as.integer(rep(0,length(gi)))
## Find the interactions in the common...with the current GI
mm <- findMatches(gi,x)
## Replace in the vector of counts for the universe, repl…
updated 5.4 years ago • Marco Blanchette
as.matrix(table_all[,1:8])
df<-data.frame(x=colnames(exp),y=c(rep(c("PB","SP"),3),"SP","SP"),row.
names=colnames(exp))
meta<-data.frame(labelDescription=c("ID","Character"))
my_set=new("ExpressionSet", exprs=exp,
phenoData=new...data=df,varMetadata=meta),
annotation="hgug4845a.db")
I created phenoData just using the name of the samples. It looks fine
(without no error!) but now my_…
updated 13.6 years ago • Yoo, Seungyeul
pre>
> bam = scanBam ("~/test.bam", param = ScanBamParam (what = c ("qname", "rname"), tag = character (0)))
> bam = scanBam ("~/test.bam", param = ScanBamParam (what = c ("qname", "rname"), tag = c ("XN", "XM")))
Warning messages:
1: In doTryCatch(return...expr), name, parentenv, handler) :
length of NULL cannot be changed
2: In doTryCatch(return(expr), name, parentenv, …
updated 7.5 years ago • Robert K. Bradley
Hi
I want to open an fastq file with readFastq() but it gives me an error :
is the invalid character a space in the file, if it is how I can remove it?
```
> f<- readFastq("a.fastq")
Error: Input/Output
file(s):
a.fastq
message...invalid character '
> sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catal…
updated 4.9 years ago • sinanoori88
<div class="preformatted">Hi,
Would it be possible to have a column (value) in a RangedData object
persist even if it has zero length?
For example,
RangedData(IRanges(), id=character())
has 0 value columns, though I think it would be nice if the 'id'
column could persist. Afterall, it is permissable to have...in a RangedData object
persist even if it has zero length?
For example,
Ran…
updated 13.9 years ago • Rob Scharpf
Hello! I am trying to look at alternative splicing using ASpli package. Below is the workflow and session info. I get an error stating "Error: vector memory exhausted (limit reached?)". Initially I tried to run this with 18 files and assumed it was the reason for error, but...splicing using ASpli package. Below is the workflow and session info. I get an error stating "Error: vector memory exhaust…
messages:
Warning messages:
1: In result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
2: In result_fetch(res@ptr, n = n) :
SQL...must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
3: In result_fetch(res@ptr, n = n) :
SQL st…
updated 5.7 years ago • Marcelo Laia
I get an error running Celaref's "contrast_each_group_to_the_rest()" (details below). Traceback() suggests the problem is related to how data is passed to MAST. This is my first time using celaref, so I guess my inputs are not correctly configured. But I can't see the issue. Can anyone offer any insights?
Thanks!
Hamid
--Details:
> cellInfoTbl <- data.frame(cellId=names(…
updated 6.7 years ago • hamid.bolouri
and basic knowledge of UNIX-like operating systems are necessary. The successful candidate must have an excellent publication record from their PhD research. In addition, she/he must demonstrate ambition to have a...complete publication list, grades of master and PhD, motivation letter, research interests and the names and addresses of three referees as one single PDF file directly to [rolf.zelle…
updated 9.4 years ago • Robert Ivanek
either
PDF or ASCII format and include the following:
* Basic information:
Title, brief description, name and contact information for each tutor,
length of the proposed tutorial.
* Audience:
Proposals must clearly identify the...available). The only
restrictions are that the program be freely available
or even open source; it must also be related to Life
Science applications. The deadline for …
updated 18.8 years ago • Thorsten Meinl
either
PDF or ASCII format and include the following:
* Basic information:
Title, brief description, name and contact information for each tutor,
length of the proposed tutorial.
* Audience:
Proposals must clearly identify the...available). The only
restrictions are that the program be freely available
or even open source; it must also be related to Life
Science applications. The deadline for …
updated 18.6 years ago • Thorsten Meinl
of how to
go about trouble shooting it:
#Error in cutree(clust.pway, k = jval) :
# elements of 'k' must be between 1 and 5
If I set removeGenes to NULL:
for ( i in KEGG.ids ) {
temp <- findSynexprs(trim(i), attractor.states)
}
The code...temp <- temp
}
}
#Error in cutree(clust.pway, k = jval) :
# elements of 'k' must be between 1 and 5
--
Sent via the gue…
find that most common sequence patters as
{A, B } = > 3
from lines 1,3,5.
Pls note that A,C,B must not be considered because C comes in between
and line 5 also must not be considered because order of A,B is
reversed.
In simple
other species in the counts matrix that is supplied to DESeq2, then supplying the other-species gene names as a vector to the `controlGenes`)? When following this approach and subsequently running `DESeq2::DESeq()`, I believe the genes
updated 3.0 years ago • kalavattam
<div class="preformatted">
Dear Gviz developers,
We have come across an issue while visualizing chromosome 16 of the
human genome hg19 using IdeogramTrack and plotTracks. Plotting chr16
produces the following error:
Error in lcS[[as.numeric(j) - 1]] : subscript out of bounds
while this does not happen with other chromosomes. Please see the
minimal example attached below.
##### beginnin…
stringdist
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
The S3 consistency warning does not return a violating function, so I'm not sure what to investigate
in data analysis and
programming in a Unix/Linux (preferably with R and Bioconductor) is a
must. Knowledge of basic biology is considered an asset.
We invite strong candidates holding a PhD in Bioinformatics or PhD...including CV, brief statement of research interests and
relevant data analysis experience, names and email addresses of at
least 2 referees before November 11th, 2012 by e-mail to
…
updated 13.3 years ago • Mark Robinson
Hello,
I am using ggbio to plot snp frequencies.
I have a following GRanges object (named lost):
GRanges object with 6 ranges and 2 metadata columns:
seqnames ranges...nbsp;<Rle> <IRanges> <Rle&a…
updated 10.9 years ago • Miss Agnieszka Aleksandra Golicz
gt;
>
> makeGRangesFromRefSNPids <- function(myids)
+ {
+ ans_seqnames <- character(length(myids))
+ ans_seqnames[] <- "unknown"
+ ans_locs <- integer(length(myids))
+ for (seqname in names(getSNPcount())) {
+ locs...value
seqnames ranges strand | RefSNP_id
<rle> <…
updated 15.0 years ago • SimonNoël
cel files using 1G of RAM and 2G of swapping
memory
and get this message
Error: cannot allocate vector of size 359894 Kb
Note that regular RMA runs just fine.
Then I read specifications for gcRMA and found recommendation...of RAM.
So I've upgraded my machine to 1.5G and got exactly the same message
Error: cannot allocate vector of size 359894 Kb.
What else could you recommend to solve the probl…
<div class="preformatted">
I am a user of XCMS for analysing LC-MS data. I have 500
samples(chromatograms) and I am getting an error message when ever I
start the analysis saying cant make a vector of some MB size.
I got the message after applying this command, it Works for some
samples but at some point it stops:
> xset...chromatograms) and I am getting an error message when ever I…
a method for function '%in%': Unknown track: rmsk"
Listing all available tracks reveals that the name for the track might be: "RepeatMasker".
```r
# List all available tracks in the session
available_tracks <- trackNames(mySession...print("Available Tracks:")
print(sort(available_tracks))
```
However, when I replace the track name "rmsk" with "RepeatMasker (see below), I still…
updated 16 months ago • Andreas.Herbst
the
following error:
Error in contrasts.fit(fit2, contrasts2) :
Number of rows of contrast matrix must match number of coefficients
In addition: Warning message:
In contrasts.fit(fit2, contrasts2) :
row names of contrasts...don't match col names of coefficients
Sorry for all these questions, initially I treated my experiment as a
2x3
factorial, after I conducted
updated 12.6 years ago • Ilario De Toma
timeout
In addition: Warning messages:
1: In result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
2: call dbDisconnect() when finished...working with a connection
3: In result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSen…
updated 4.9 years ago • Imad
<div class="preformatted">Hi ,
I need a Granges object with exons data for few chromosomes, i got
Granges
list of transcripts and their exons as follows:
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
txdb<-TxDb.Hsapiens.UCSC.hg19.knownGene
tx_Exons<-exonsBy(txdb)
1-How to use reduce on Granges list?how to get the unique exons only
and
exclude redundant exons?
2-How to se…
updated 11.4 years ago • Asma rabe
lt;IRanges> <Rle> | <factor> <integer> <integer> <integer> <character> <IntegerList> <character> <CharacterList>
[1] chr19 572764 + | intron 63 63 82 1 <NA> BSG <NA>…
updated 7.5 years ago • goldberg.jm
in .validity_check_alias(this_row[, alias]) :
Q4: CD4-FITC-H- , CD8-PE-H-contains illegal character: |,&,:,/
error.
I think the error is self descriptive, i.e. it's because of the colon character but it would seem to me
updated 8.3 years ago • biomiha
<div class="preformatted">Dear list,
I would like to have a look at the code of summarizeOverlaps,
so I compute:
library(GenomicFeatures)
showMethods("summarizeOverlaps",includeDefs = T)
Function: summarizeOverlaps (package GenomicRanges)
features="GRanges", reads="GappedAlignments"
function (features, reads, mode = Union, ignore.strand = FALSE,
..., param = ScanBamParam())
{
mod…
updated 13.8 years ago • Stefanie
I have a pair of chipseq. One is really bad. Mapping failed.
I was wondering if it's possible to analyse only one without the pair ?
Other question :
I tried to do the analyze with both of the samples even is one is not very good.
I did two different things : the first time I set the rule that peaks must be in both replicates...that gaves me 1116 differential peaks.
<pre>
db…
updated 8.3 years ago • ZheFrench
Time)
> fit = lmFit(data_to_model, design)
Error in rowMeans(y$exprs, na.rm = TRUE) : 'x' must be numeric
> design = model.matrix(~ fac1 * fac2 * data_to_model$Time *
data_to_model$Value)
> fit = lmFit(data_to_model, design...Error in rowMeans(y$exprs, na.rm = TRUE) : 'x' must be numeric
fac1 is a factor
fac2 is a factor
data_to_model$Time is a numeric
my data_to_model data…
updated 14.5 years ago • Dimitris Kampas
signal around gene, but it gave error like this:
Error in intoNbins(gr, bcount) : all 'width(gr)' must be >= 'n'.</pre>
My command is :
<pre>
mg <- metagene$new(genes, "H3K4me3.bam", cores = 8, force_seqlevels = TRUE)</pre>
After add the parameter...besides, some times it gave error "</pre>
<pre>
Error in intoNbins(gr, bcount) : all 'width(gr)…
updated 8.1 years ago • Wojeff
of this function
bwss <- function(x,group).
the docu. explains they are:
x: a numeric vector giving the responses.
group: a vector or factor giving the grouping variable.
For example, I have a microaray dataset
the problem is that your class labels (rmadata2$Genotype)
are
a
> factor, but they should be a vector of integers starting at 0.
>
> The help for mt.maxT says:
> "classlabel: A vector of integers corresponding to observation...column)
> class labels. For k classes, the labels must be integers
> between 0 and k-1."
>
> Yo…
character.only = TRUE)
library(organism, character.only = TRUE)
sorted_dfx <- cluster_df$coef20
names(sorted_dfx) <- cluster_df$cluster_df
sorted_dfx <- sort(sorted_dfx, decreasing = TRUE)
keytypes(org.At.tair.db)
gse...sign") + facet_grid(.~.sign)
Error in unique.default(x, nmax = nmax) :
unique() applies only to vectors
### SORTED DFX
> head(sorted_dfx)
AT2G199…
updated 3.5 years ago • rama
PileupBuffer.h:5:15: error: set: No such file or directory
PileupBuffer.h:6:18: error: vector: No such file or directory
PileupBuffer.h:7:19: error: utility: No such file or directory
PileupBuffer.h:8:21: error: algorithm...std::make\_pair' has not been declared
PosCache.h:28: error: ISO C++ forbids declaration of 'vector' with no type
PosCache.h:28: error: invalid use of '::'
P…
updated 10.7 years ago • Spollen, William G.
Unable to complete analysis.
Warning messages:
1: No contrasts added. There must be at least two sample groups with at least three replicates.
2: No contrasts added. There must be at least two sample groups
updated 2.8 years ago • Chris
part is not giving any problems, but in the second part I get an error that a uniquely valid column must be specified. It is actually an existing column, so I don't understand why it is not valid. Does anyone have a clue?
```
# Data merge...by.x="Sample_Name", by.y="row.names", sort = FALSE)
Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column
updated 4.5 years ago • FWNL15
called
'gpllibrary'
library(gpllibrary[1])
# Error in library(gpllibrary[1]) : 'package' must be of length 1
library(as.character(gpllibrary))
# Error in library(as.character(gpllibrary)) :
# 'package' must be of length
to NA.
> de.com <- exactTest(d)
Error in if (any(dispersion < 0)) stop("dispersion must be non-
negative") :
missing value where TRUE/FALSE needed
> de.com <- exactTest(d,dispersion=0)
Error in binomTest(s1[pois...s2[pois], p = n1/(n1 + n2)) :
y1 and y2 must be non-negative
[[alternative HTML version deleted]]
</div
I am not sure what the right protocol is for reporting bugs in ExperimentHub, but here we go. It appears that the dataset ExperimentHub()\[\["EH359"\]\] (apparently a.k.a. curatedMetagenomicData::ZellerG\_2014.marker\_abundance) is an ExpressionSet whose exprs is a matrix of __characters__. The matrix can be converted to numeric, and all elements seem to represent legitimate numbers, but I wonder…
updated 9.1 years ago • Wolfgang Huber
G'day all,
I don't want to be trouble (I'm new to the list), but this is causing
us some problems too - is it safe to assume a message will be posted
when it is fixed?
thanks for all the good work - we use this package all the time - on
Mac OS X and FreeBSD
cheers
Ben
--
Ben Madin
AusVet Animal Health Services
P.O. Box 5467
Broome WA 6725
Australia
t : +61 8 9192 5455
f : +61 8 9192 55…
Hello everyone
I'm trying to use readComp from systemPipeR, but I get an error that I don´t know how to solve.
I'm using:
cmp <- readComp(file="targets.txt", format="matrix", delim=",")
My targets.txt looks like:
FileName SampleName Factor description
1 5WOU1.txt 5WOU1 Orn Undis
2 5WOU2.txt 5…
updated 7.1 years ago • catscampos
Excellent, thank you so much for your help Herv?.
cheers
Ben
On 30/04/2009, at 3:52 AM, Hervé Pagès wrote:
> Hi Ben,
>
> This is fixed in RdbiPgSQL 1.18.1 (release) and 1.19.1 (devel).
> As usual, please expect about 24 hours for these new versions to
> propagate to the BioC public package repositories. Then install with
> biocLite().
>
> Cheers,
> H.
>
>
>…
negative integers
what does it mean exactly?
maybe that the column range (e.g chr1 1000-1002) must be End - Start > 0?
this is my object **ce**
> ce
A CAGEexp object of 1 listed
experiment with a user-defined name and respective...5
metadata(0):
assays(2): counts normalizedTpmMatrix
rownames: NULL
rowData names(3): genes annotati…
updated 5.7 years ago • mirkocelii
must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
6: In result_fetch(res@ptr, n = n) :
SQL statements...must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
9: In result_fetch(res@ptr, n = n) :
SQL statements...must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery()…
updated 5.5 years ago • Marton Papp
Hello everyone:
I would like to add "ORF IDs to Chromosomal Location" to my data frame named genes in the DGEList-object.
The organism is yeast, and I downloaded org.Sc.sgd.db..
```
> columns(org.Sc.sgd.db)
[1] "ALIAS...data package
org.Sc.sgdALIAS Map Open Reading Frame (ORF) Identifiers to Alias Gene Names
org.Sc.sgdCHR Map ORF IDs to Chromosomes
org.Sc.sgdCHRLENGTHS…
updated 2.1 years ago • Chih
from a peak list where start is the
start
of the binding site, end is the end of the binding site, names is the
name
of the binding site, space is the chromosome name where the binding
site is
located.
If you think having a conversion...3123260, 3857501, 201089), end = c(967754, 2010997,
2496804, 3075969, 3123360, 3857601, 201089), names = c("Site1",
"Site2", "Site3", "Site4", "Site5", "Site6…
1,ID="P
robeName")
Error in order(na.last, decreasing, ...) :
argument 2 is not a vector
I didn't think argument 2 was meant to be a vector
Using default values gives me the same result:
> MA2 <- processCGH(MA1...ID="ProbeName")
Error in order(na.last, decreasing, ...) :
argument 2 is not a vector
My MA1$genes seems to be set up ok:
> colnames(MA1$genes)
[…
updated 18.3 years ago • jhs1jjm@leeds.ac.uk
data from GEO148000, [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148000][1]
The IDAT file names from this project are like
GSM4452048_Asthma_9_Grn.idat,
GSM4452048_Asthma_9_Red.idat,
GSM4452049_COPD_1_Grn.idat...with my file? Do the red and green idat files have to have the Array and slide values in the file names?
[1]: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148000
updated 3.1 years ago • minardsmitha
return to the series' gothic and medieval roots, employing richly detailed environments and menacing character designs to Diablo 4 Gold evoke a haunting atmosphere. The interplay of light and shadow heightens the game's foreboding...Entertainment plans to support Diablo 4 with regular updates and expansions, introducing new regions, character classes, storylines, and seasonal events to keep the w…
updated 13 months ago • aventurinele
I'm looking for promoters for protein coding transcripts in GRanges, and I end up with lots of NA values in my protein_id metadata column. Is there a way to remove the rows corresponding to the metadata column containing NA?
```
> ahub <- AnnotationHub()
> query(ahub, c("GRanges","Homo sapiens","GRCh38"))
> ahub['AH28674']
> gtf <- ahub[['AH28674']]
…
fdef, mtable) :
unable to find an inherited method for function ‘peakDetection’ for signature ‘"character"’
Whole function:
>bam <- system.file("extdata", "ENCFF653KEU.bam", package="nucleR")
> reads <- readBAM(bam, type="paired...fdef, mtable) :
unable to find an inherited method for function ‘peakDetection’ for signature ‘"character"’
Ha…
updated 6.1 years ago • anne.kannengiesser
entry, I tried to
"post the article."
First I got a message that there were lines longer than 80 characters.
OK.
The feedback was a bit rude, but I can deal...
I went back and manually edited all the lines
(for whatever reason, the...window in post.gmane.org/post.php
displays lines that are longer than 80 characters).
I then tried to post again.
This time I got nonsense about how I was
"top po…
updated 20.1 years ago • david clayton
k x y z ir r
<integer> <numeric> <integer> <character> <iranges> <rle>
1 2 -0.8 1 E 1-10 1
2 2 -0.43 2 U 2-11 5
3 2 -0.67 3 U 3-12 4
4 1 0.58 4 L 4-13 2
…
over that value (1) or not (0). Then i have to compare this data with a known enhancer clasification vector with 0 and 1 and see the best coincidence between my rna data and this vector
![enter image description here][2]
But always
phyper(x-1, m, n-m , k, lower.tail = FALSE)
# x: number of sample genes at GO node (can be vector with many
entries)
# m: number of genes at GO node (works with vector of same
length
as x)
# n: number of unique genes at all GO nodes
Recent ...
Replies
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I updated the above answer today.
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@gordonsmyth Noted, thank you very much.
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