require(RBGL)" I get the error message that: "Failed with
>>> error: ??'graph' is not a valid installed package?".
>>
>> Installing a package is not that simple. ?R does various processing
when
>> taking the
Order by: Relevance
KEGGgraph are the entry IDs 12801 and 13489, but what I would like to get are the associated gene names (Cnr1 and Drd2).
I did the following:
library(KEGGgraph)
tmp <- tempfile()
retrieveKGML(pathwayid='mmu04015' , organism='mmu...destfile=tmp, method="wget")
pathway <- parseKGML(tmp)
nodes\[\[60\]\]@name\[\[1\]\] ---> retrieves mmu:12801
nodes\[\[60\]\]@n…
updated 9.8 years ago • Osvaldo
assays = SimpleList(counts = countData), :
the rownames and colnames of the supplied assay(s) must be NULL or
identical to those of the SummarizedExperiment object (or derivative)
to construct
Calls: sourceWithProgress
updated 4.0 years ago • sfpacman
Info: setting summary
------------------------------------------------------------
Name of aligned read file: SRR3105506.sorted.filtered.bam
Aligned read file format: BAM
Directory of processed bin-level...files: ./jmosaics/
Construct bin-level files by chromosome? N
Is file for chromosome info provided? Y
Name of file for chromosome info: hg19.chrom.sizes...informa…
updated 7.9 years ago • james.dalgleish
the relevance of Bioconductor
and the BioC2006 conference to the applicant's research.
Applications must be provided on a single page in PDF or RTF
format with indication of name, e-mail address, scholarship track
(student-contributor...developer-contributor, international
student-contributor), text of essay, word count. Applications
must be e-mailed to biocworkshop at fhcrc.org
Applications mu…
updated 19.5 years ago • Vincent J. Carey, Jr.
Raphael,
I week ago there was an new release of Ensembl and a few of attributes
in
Ensembl changed names. These changes have been fixed in the
GenomeGraphs
package available here:
http://bioconductor.org/packages/2.3/bioc...gt; structure_exon_rank
> Please use the function 'listAttributes' to get valid attribute
names
> >
>
> For you information, I use R 2.7…
updated 17.3 years ago • steffen@stat.Berkeley.EDU
gt;>>> I use the following code to do RMA. I'm wondering how get the
probe
>>>> level values before the summary to the probeset level values.
>>>>
>>>> library(oligo)
>>>> data<-read.celfiles
updated 15.9 years ago • Benilton Carvalho
on how the die comes up and how much it rains.
The difference between BH and BY is that BY is valid for any level of dependence between genes while BH is theoretically valid only for weak or no dependence. Hence
after a feature selection step using limma,
including the
whole procedure in the cross-validation.
Before finding the CMA package I had implemented myself the same
procedure
(cross-validation of feature selection...different from zero
gives us the
information that the gene is actually expressed at a certain level,
making
us more confident that what is observed is not noise?
In s…
updated 16.8 years ago • Renaud Gaujoux
<div class="preformatted">Hi Nico,
Sorry it's taken awhile to get back to you. I wanted to ask about what
behavior you'd expect from a call to unique() on a DNAStringSet, i.e.,
what is your use case?
unique() on a named character vector drops names:
chr <- c(a="A", c="C", aa="A", c="CC")
> unique(chr)
[1] "A" "C" "CC"
Same for a named list:
lst <- list(a="A", c="C…
updated 13.1 years ago • Valerie Obenchain
biomart in the "attributes" section, and some of the results are returned with this style chromosome name "CHR\_HSCHR19\_2\_CTG2". How can I correct this?
<pre>
library(biomaRt)</pre>
<pre>
#get annotations for processed transcripts
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...gt;Species1", ">Species2", ">Species3" etc. to "1", "2", "3"... I would like to keep the name of at least one of the sequences that have been collapsed together, rather than have them renamed to numbers. Is it possible.…
updated 5.8 years ago • al.gar.aber
paste, x),])</pre>
I have this error:
<pre>
Error in do.call(paste, resGR) : second argument must be a list</pre>
Perhaps my attempt is not feasible, but it works well if use data.frame. Is there any simple and vectorized
updated 8.8 years ago • Jurat Shahidin
info
pheno <- read.csv('pheno_sheet.csv', header = T, row.names = 1L)
# making sure the row names in colData matches to column names in counts_data
all(colnames(data) %in% rownames(pheno))
## [1] TRUE
# are they in the same order...ENSMUSG00000028180 ENSMUSG00000028182 ...
## ENSMUSG00000036958 ENSMUSG00000042678
## rowData names(0):
## colnames(13): Control_1 Control_2 ... Treatmen…
updated 3.7 years ago • Manav
a bioconductor package) for converting a column of Uniprot IDs to their corresponding protein names using RStudio. But I'm still not able to see the names changing. I'd appreciate it if someone can have a look at my code and...ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
# Get the protein names using biomaRt
search_ids <- c("protein")
protein…
updated 2.7 years ago • a.a.houfani
Thanks,
Becky
===========R Console =================
> x <- readPlateList("plateList.txt", name="Automated Preliminary
Analysis", path=dataPath)
Automated Preliminary Analysis: found data in 8 x 12 (96 well) format.
Reading...Error in plotScreen(ldat, zrange = range(mtW), fill = wellCols, nx =
pdim(x)[["ncol"]], :
'fill' must have length >=2 since it is used to compute…
Hi,
I am a relatively novice bioinformatician and want to perform differential expression on my RNASeq data (12 treatment groups with 6 replicates of each). I have built a sample table:
```
Sample_Table <- data.frame(Sample = samples,
FileName = files,
Treatment = Treatment,
Cell = Cell,
…
updated 5.7 years ago • bak16
KO LPS C
The main contrasts that i want to analyze are:
-the difference in basal levels of proliferating cells (KO.P-WT.P)
- the difference between genes activated by LPS in KO vs WT:
(KO.LPS-KO.U) - (WT.LPS -WT.U...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 con…
updated 12.5 years ago • Ilario De Toma
div class="preformatted">Hello list
Is there a way to plot chromosome band names along an ideogram using
genome
graphs. I realize that this can be done in quantsmooth but I prefer
the
ideograms generated
updated 14.4 years ago • Pete Shepard
design\_NCaF, design = ~Groups1 + Patient)
It gives me following error message
<pre>
factor levels were dropped which had no samples
Error in checkFullRank(modelMatrix) :
the model matrix is not full rank, so the model...variables or interaction terms in the design formula are linear
combinations of the others and must be removed.
Is it because of remaining two group…
updated 8.0 years ago • Björn
following error:
Error: 2 errors; first error:
Error in array(x, c(length(x), 1L), if (!is.null(names(x)))
list(names(x), : 'data' must be of a vector type, was 'NULL'
I have included the complete output of my attempt to run the vignette...with SYMBOL...
Error: 2 errors; first error:
Error in array(x, c(length(x), 1L), if (!is.null(names(x)))
list(names(x), : 'data' must be of a vector type…
updated 11.5 years ago • Guest User
gt; Even for a very simple reaction like:
>>
>>
>> re<-new("Reaction",id="r1",name="r1",kineticLaw=new("KineticLaw",ma
th=as.expression(parse(text="(A)"))),reactants=list(new("SpeciesRefere
nce",species="s1",stoichiometry...rsbml_perform_check",
>> > so I changed line 5 in SBML.R and set the variable
"valid" to
>…
something that I don't know how to do.
I would like to compare the methylation pattern at the gene level with and without the condition, for this I do a differential methylation analysis, for example:
```r
se <- SummarizedExperiment...summaryExtractTest(summary)
```
And now I would like to look at what happened at the gene level, one way is to do something like this
```r
df <-…
updated 14 months ago • ramiro.barrantes
sam.out, 3, file = "", gene.names =
nrow(data)[[1]],
:
The length of gene.names must be equal to the number of genes.
I know it must be a silly mistake somewhere.. but I'm unable to figure
it
out.
I used a dataset...22622 genes and 40 samples, where the first column
lists
the clone ID ad the second column lists the names, continued with the
rest
40 samples.
With my original data, I gave…
updated 18.6 years ago • Ruma Sanyal
I really like the features that are provided in karyoploteR.
https://bioconductor.org/packages/release/bioc/html/karyoploteR.html
But, I am working with different organisms. I am able to find the organisms of interest using:
> available.genomes()
<code> [1] "BSgenome.Alyrata.JGI.v1" &nbs…
updated 8.1 years ago • kirannbishwa01
div class="preformatted">Hello,
In working with HTqPCR lately I noticed that the gene/feature names
are not produced in the output of limmaCtData, even if they are
present in the input. This isn't an issue with ttestCtData...puzzled by how I would annotate multiple
comparisons, so it would definitely be helpful if the gene names
appeared in the output. Unless I'm doing something wrong, but tha…
2): counts avgTxLength
`` dds <- DESeq(ddsTxi) ``
estimating size factors
Note: levels of factors in the design contain characters other than
letters, numbers, '\_' and '.'. It is recommended (but not required...only letters, numbers, and delimiters '\_' or '.', as these are safe characters
for column names in R. \[This is a message, not an …
the ROWNAMES and the COLNAMES in the initial numerical matrix/dataframe,
and use identical NAMES (as the ROWNAMES and COLNAMES) in the HeatmapAnnotation() dataframe for precise annotations ?
I am asking the question
updated 8.2 years ago • Bogdan
Hi I am doing the following to get the tximport count matrix with gene name in the first column
<pre>
txdf <- transcripts(EnsDb.Mmusculus.v79, return.type = "DataFrame")
txdf$symbol <- mapIds(EnsDb.Mmusculus.v79
updated 8.1 years ago • tanyabioinfo
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
But the two elements of my design are the two columns in my colData:
```
pData(set_NHP_RUVg)
key_IP_mf.Treatment
Hi,
I currently am using a dataset with 5 timepoints and 4 replicates per timepoint. While the results file exports the L2FC, I am also interested in extracting the numerator log2 values for each time point. I have already extracted the log2 normalized counts for each individual sample with the code below, but am unable to find a way to extract the log2 mean normalized counts for each level/ tim…
updated 7.2 years ago • agdif
area" in Excel (from a sheet without " "
in
it's name) will give an additional line in sqlTables that is of
table_type "TABLE", but I can't read it neither. A closer look
revealed...that odbcConnectExcel() reads such sheets with " " in the sheet-name
as
?TABLE? (as it does for "print areas") while sheets without (eg
?Sheet1?) are read as ?SYSTEM_TABLE?. Is this the reason why
sqlQuery...solution …
updated 19.0 years ago • Wolfgang Raffelsberger
<div class="preformatted">Hello all,
I am trying to repeat a hypergeometric test 40 times by putting it in
a
loop, but I am missing something as it does not work.
How do I substitute a slot name with a string variable?
Here is the code so far:
> probTable <- data.frame(row.names=rownames(repData))
> for (dataset in...by putting it in
a
loop, but I am missing something …
updated 15.4 years ago • Edwin Groot
In going through the user guide vignette for derfinder and looking up function docs for more details, I came across the suggestion that the chromosome naming style and the species should be specified, either as arguments to certain commands, or globally for the session. It feels...and looking up function docs for more details, I came across the suggestion that the chromosome naming style and the …
updated 8.3 years ago • fruce_ki
<div class="preformatted">Dear 'conductors,
I am trying to get a mapping from Agilent mouse microarray probes to
ENSEMBL gene ids for further analysis.
>library("mgug4122a.db")
>data = "path to data" ## This is data produced from an initial
analysis of an Agilent hybridization
>dat <-read.table(data,sep=",",header=TRUE)
>pro = as.character(dat[,3]) …
updated 16.4 years ago • peter robinson
I found that browseGenome in the rtracklayer package fails if the ranges supplied have names. This works:
<pre>
> ir <- IRanges(20000, 50000)
> track <- GRangesForUCSCGenome("hg19", chrom="chr22", ranges=ir)
> browseGenome...with 1 views and 181 tracks
</pre>
This does not work:
<pre>
> ir <- IRanges(20000, 50000, names="a…
updated 10.3 years ago • Stephanie M. Gogarten
and
Computational Biology. Appointments
will be made at the ASSISTANT, ASSOCIATE and FULL PROFESSOR levels.
Successful candidates will join
an innovative and multidisciplinary Institute of Integrative Genome
Biology...programs, have a strong commitment to excellence in teaching
at the undergraduate and graduate
levels, and participate in departmental and interdepartmental graduate
programs. Appli…
updated 19.2 years ago • Thomas Girke
loadImages` function from cytomapper.
> dataset
CytoImageList containing 48 image(s)
names(48): 1_A3 1_A4 1_A5 1_A6 1_A7 1_A8 1_B1 1_B2 1_B3 ...
Each image contains 47 channel(s)
channelNames(47): 104Pd_104Pd.ome 113In_113In_HLA...115In_115In_CD11c.ome ...
> display(dataset[[1]])
Error in validImage(x) : object must be an array
> clas…
updated 16 months ago • Dario Strbenac
dds <- DESeqDataSet(rse_gene, design = ~some_condition) # some_condition is a random name, it is not in the data.
```
It fails with:
```
Error in DESeqDataSet(rse_gene, design = ~some_condition) :
all variables in design formula...must be columns in colData
```
With a plain counts file, I add this column after loading to the data.frame and everything works
I imported a data as follows which has first column as genes name and other 21 columns for samples with respective counts for genes using >d=read.csv("path/xyz.csv", as.is=T)
THEN, define...this step, I get an error message as follows
<pre>
"Error in .isAllZero(counts) :
count matrix must be integer or double-precision"</pre>
What is the problem as how to solve it ?
&a…
updated 7.7 years ago • Björn
relevel(myfac, ref="A")
design <- model.matrix(~myfac)
colnames(design) <- as.character(levels(myfac))
v <- voom(dge,design,plot=TRUE)
fit <- lmFit(v,design)
fit2 <- fit[,as.character(levels(myfac))[-1]]
fit2 <- eBayes(fit2
<div class="preformatted">
Hello dear List,
when I save a cpm table (ordered by p-value for example) , I do not
have the names of the genes but only cpms. How can I add them ?
I used :
> o <- order(lrt$table$PValue)
> tab <- cpm(y)
> write.table(tab, file="CPM.txt...Hello dear List,
when I save a cpm table (ordered by p-value for example) , I do not
have t…
updated 13.1 years ago • Guest User
I have made a Contrasts matrix as
design <- model.matrix(~0+f)
colnames(design) <- levels(f)
design
fit <- lmFit(eset,design)
names(fit)
cont.matrix <- makeContrasts(C9T9="Control9-Treated9",C24T24="Control24-Treated24",........................................,levels=design)
cont.matrix
fit2 <- contrasts.fit(fi…
updated 8.9 years ago • rkp
at normalization data step and i obtained normalized counts matrix, How can I change Ensemble gene name into common gene name
updated 8.1 years ago • salvocomplicazioni1
div class="preformatted">Estimated colleagues,
I am working with CGH data. I have the name of the BAC clones and
their
chromosome locations. They correspond to OncoBAC arrays (?).
Is there any way in bioconductor
IS Project Manager/ Day/ 40 Hrs/ Channing Division of Network Medicine - (3133887)
Description
This position includes both project management and advanced software development. The successful applicant will perform multidisciplinary work in data science, clinical trials, and cloud computing. Our group is centrally involved with the Bioconductor project, a 20-year open source/open development…
updated 4.8 years ago • Vincent J. Carey, Jr.
so asking to replace NAs or empty positions by a character string is a wrong code, since the level "unresolved" doesn't exist.
vj[is.na(vj) | vj == ""] <- "unresolved"
So the piece of code above must be introduced after the
updated 8.7 years ago • omran.allatif
0 rows into table pmfeature... Error in
sqliteExecStatement(con,
statement, bind.data) :
bind.data must have non-zero dimensions
> traceback()
8: stop("bind.data must have non-zero dimensions")
7: sqliteExecStatement(con, statement...like this.
Error in read.xysfiles2(channel1 = file.path(path, files2Ut), channel2
=
file.path(path, :
Must install the pd.100929.hg19.deluxe.prom.meth.h…
updated 12.3 years ago • Nitesh Turaga
through multiple layers of biology, through robust statistical modeling followed by experimental validation in human stem cell culture. The position will involve analysis and modeling of multi-omics datasets (genotype...ATAC-seq, RNA-seq, cellular phenotypes), and integration of additional cohorts and datasets (tissue-level and disease phenotypes). The work will connect closely with multiple inte…
with 258508 rows and 1 value column across 240 spaces
space ranges | name
<factor> <iranges> | <character>
1 chr1 [ 564401, 570399] | 2726
2 chr1 [ 756001, 758799] | 76
3 chr1 [ 811201, 811799] | 34
4 chr1 [ 821801, 826199...12809
258508 chrY [ 5…
updated 12.6 years ago • Guest User
a count matrix for an RNAseq experiment. I have aligned paired-end .sam files sorted by read name and have specified the -p flag and the −−countReadPairs parameter (please see code below). When I run the command, I get ERROR...if the −−countReadPairs is not included but as I understand it, in version 2.0.2, −−countReadPairs must be included in order to get counts by fragments (as opposed to earli…
updated 4.4 years ago • s.muroy
following error when running a specific dataset
module <- runFastHeinz(subnet, scores)
Error in names(best.path) <- names.list :
'names' attribute [18] must be the same length as the vector [6]
-- output of sessionInfo():
R version 3.1.0
updated 11.6 years ago • Guest User
<div class="preformatted">
-----Original Message-----
From: News@bioinformatics.org [mailto:News@bioinformatics.org]
Sent: Thursday, July 29, 2004 2:34 PM
To: Lapointe, David
Subject: [BiO News] Gene name errors introduced by Excel
A research article at BMC Bioinformatics:
BACKGROUND:
When processing microarray data sets...Sent: Thursday, July 29, 2004 2:34 PM
To: Lapointe, David
Subject…
updated 21.4 years ago • David Lapointe
Pediatrics and more
16 different sortable fields
Database of American Pharma Companies
47,000 names and emails of the major positions
Listing of US Hospitals
Complete contact information for the important jobs held...391 for all 5 datasets
send and email to: sheilaprimanzon at hotmail.com
this offer is only valid until March 28, 2008
</div
updated 17.7 years ago • cockatoo
mart, dataset = dataset, verbose = verbose)
:
The given dataset: hsapiens_gene_ensembl , is not valid. Correct
dataset names can be obtained with the listDatasets function.
has anyone come across the same problem?
Many
updated 14.4 years ago • Yan Jiao
First,the ensemble-based gtf file that I used to align all my mouse RNAseq data has the chromosomes named as “1, 2 , 3”… Rather than “chr1 , chr2 ..”. My Testing R code for summarizeOverlaps is as follows:
<pre>
library(TxDb.Mmusculus.UCSC.mm10.ensGene...sqlite I am using has chr1, chr2 .. Format
seqinfo(bamLst_grp1) #this shows that the chromosome names for my testing bam …
updated 9.9 years ago • bioprog
div class="preformatted">I would like to know how to evaluate a character string as a variable
name
in R. Specifically, I need to "compute" the variable name in the
phenoData
slot of an ExpressionSet object.
> varLabels(sample.ExpressionSet...is interpreted as a character string by R, but I need
for
it to be evaluated as a variable name. Seems straightforward, but I
couldn't
figure it …
updated 16.6 years ago • Kavitha Venkatesan
Error in wilcox.test.formula(organ8w$epiWAT ~ as.integer(group), data
=
organ8w) :
grouping factor must have exactly 2 levels
my code is,
head(organ8w)
Group Liver Spleen LV RV Gastrocnemicus
Soleus
rpWAT epiWAT BAT
1 Control...ED
[22] HFD-M HFD-M HFD-M HFD-M HFD-M HFD-M HFD-M HFD-M
HFD-M
HFD-M HFD-M HFD-M
Levels: Control HFD-ED HFD-M
Mann-wit…
updated 11.5 years ago • Nikul Soni
single cell simulated data. I need to have a variability in samples which means that expression levels of genes should change across samples. I have 100 samples, 20 genes, 5 cell types and my code to generate single cell data...1-Is there any other way that I can generate 100 samples?
2-Also, I want that gene expression level of genes change between individual samples. for example, gene expres…
updated 4.1 years ago • Fatima
Loading required package: reposTools
Loading required package: tools
Error in Bundle(x) : No slot of name "Bundle" for this object of class
"localPck".
I must say that I dearly love the good ship Bioconductor and all who
sail in it
updated 21.0 years ago • michael watson IAH-C
Recent ...
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