experiments. Now I am trying to
find to over which genes these peaks overlap (and extract the gene
name).
I'm sure this should be pretty easy, but I am just starting with
bioconductor, so some concepts are still vague.
Here's what
Order by: Relevance
object with 24848 ranges and 8 metadata columns:
seqnames ranges strand | name score_log2FC signalValue_log2FC pValue_.log10pval qValue_.log10FDR
<rle> <iranges> <rle> | <character> <numeric> <numeric...packages that do?
Thank you in advance for your help.
</numeric></numeric></numeric><…
updated 2.7 years ago • C T
language R
library(hgu133plus2.db)
x=hgu133plus2ENTREZID
xx=as.list(x)
basefile=data.frame(names(xx),as.character(unlist(xx)))
write.table(basefile,"Basefile.txt",sep="\t",row.names=F)
library(AnnBuilder)
mySrcUrls=getSrcUrl...invalid object for slot "baseFile" in
class
"UG": got class "data.frame", should be or extend class "character"
Calls: ABPkgBuilder ... UG -> new -> i…
updated 17.4 years ago • Kamila Naxerova
<div class="preformatted">Hi everyone,
I have recently posted a query names "How to use ExpressionSet for
further
Analysis"(http://article.gmane.org/gmane.science.biology.informatics.c
onductor...div class="preformatted">Hi everyone,
I have recently posted a query names "How to use ExpressionSet for
further
Analysis"(http://article.gmane.org/gmane.science.biology.informatics.c...argume…
updated 16.4 years ago • Md.Mamunur Rashid
gt; (txdb <- makeTxDbFromGFF(gtffile, format="gtf",circ_seqs=character()))
<strong>Import genomic features from the file as a GRanges object ... OK</strong>
<strong>Prepare the 'metadata' data frame...in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery': Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : </strong>
…
updated 10.2 years ago • JunLVI
shows me this error -
Error in as.list.default(X) :
no method for coercing this S4 class to a vector
I haven't made any changes in the script, so I don't know why am I getting this error.
Code should be placed in three backticks...as shown below
```r
RKO_BV2_GOBP = enrichGO(gene = names(GO2), OrgDb = org.Mm.eg.db, universe = uni, readable = T, ont = "BP", pvalueCutoff= 0.05, q…
updated 3.3 years ago • estafana.t98
run DMRcate with a dataset downloaded from a paper. This dataset consist, instead of a set of probe names and their corresponding beta values, of a set of genomic positions and their corresponding beta values.
When I run `cpg.annotate
updated 5.3 years ago • Jeni
my data file with all beta values for each sample and CpG - it is a matrix with rownames = cpg names as character and columnames = samples names as character
my design file is named characteristics with sample names...characters) and group in which each sample is in and some other general patient information like age and gender
m=annotation...file containing the Cpg names (characters) with corr…
updated 9.6 years ago • fleur_p90
simple solution wherein I can convert the .h5 file into an R data frame or data table and have gene names added as a separate columns or as row names.
I came up with this solution but wondering if this works?
I am assuming here
updated 2.1 years ago • Sitapriya
<div class="preformatted">Dear BioC,
I tested the combineAffyBatch function in the matchprobes library to
merge data from
HG-U133A and HG-U133Av2 GeneChips, which seemed to work well for small
number of arrays.
> f1 <- list.files(path=dir1,".CEL",ignore.case=T,full.name=T)[1]
> f1file <- list.files(path=dir1,".CEL",ignore.case=T,full.name=T)
> pd1 &am…
updated 16.9 years ago • Oura Tomonori
results in__ the call to the first inherited method.__
<pre>
setClass(
"A",slots = c(slot1 = "character")
)
setMethod(
f = "show",
signature = "A",
definition = function(.Object) {
print("Show class A")
}
)
setClass(
"B",slots = c(slot1 = "character...function(.Object) {
print("Show class B")
}
)
setClass(
"C",slots = c(slot1 = "character"),co…
updated 7.3 years ago • stolarczyk.michal93
Hello,
How can I figure out this?
Thanks in advance!
> head(huang\_group\_list)
x
1 549\_repair.bam
2 6\_repair.bam
3 …
updated 7.7 years ago • yueli7
the
gpr
file was read with marray package, next background was corrected using
smida which returns a vector. When the vector was assigned back to
marray@maRf, I got an error in checkSlotAssignment. But I can do it
element-wise (e.g...marray@maRf[1]<-vector[1],
marray@maRf[2]<-vector[2], etc.).
YJ Zhang
[[alternative HTML version deleted]]</div
updated 20.8 years ago • Zhang, Yuanji
Hi,
I have 4 vectors of the same length. I joinded them in a matrix in which every row is a vector, with the command:
<pre>
TOT=do.call(rbind...list)</pre>
in which TOT is the final matrix and list is a list with the 4 vectors.
<pre>
</pre>
Then i use normalize.quantiles on this matrix and i get this error
<pre>
Error in normalize.quantile…
updated 10.5 years ago • gugpuccio
Hi there,
I googled the question, but could not find an answer that can solve my question, so I post it here.
Thank you so much in advance!!
I recently received a dataset that has already been sequenced. The idea was: for each batch of cell, transfected with one **control** vector and a bunch of **gene overexpression** vector. So, in batch one, I have **one control vector** and **si…
updated 6.6 years ago • timedreamer
My dataset: 3 different cell types, with 3 replicates each
Cell_type is the factor and "Alveolar_macrophages" "Interstitial_macrophages" "T_cells" are the factor levels.
I created the DESeq object:
```
>dds <- DESeqDataSetFromMatrix(countData = only_counts,
colData = sample_info,
design= ~ Cell_type)
```
…
updated 5.3 years ago • paula.vaccarello
rn<-paste(data1[,1], sep="")
P_values=data1[,-1]
names(P_values)<-rn ####creating named vectors
P_values ### this contains probeID with corresponding p-values
2810273 5720014
updated 12.3 years ago • Guest User
<div class="preformatted">Hi Juan,
> Dear Heidi,
>
> My name is Juan Fernandez-Tajes and I?m using HTqPCR for analyzing
some
> Biomark 96*96 data. When I tried the following command I got an
error:
>
>>raw1 <- readCtData(files="Prueba_Blanco001.txt", format="BioMark",
>> n.features=96, n.data=96)
> Error en `$&…
tab<-b
mat<-normalize.quantiles(as.matrix(mat))
colnames(mat)<-c
rownames(mat)<-r
dates=vector("character",ncol(mat))
for(i in seq(along=dates)){
tmp=affyio::read.celfile.header(file.path("celfies",tab[i,1]),
info="full")$ScanDate
with 3 rows and 1 value column across 2 spaces
space ranges | strand
<character> <iranges> | <character>
1 chr1 [17563082, 17605866] | +
2 chr1 [61191807, 61290544] | +
3 chr2 [21920042, 21956374] | +
But then combine...with 9974 rows and 1 value column across 1 space
space …
updated 15.2 years ago • Sheena Scroggins
KEGG pathway, via the R package pathview:
i used the following code, where genes\_change is a vector of log fold changes with names as the EntezGene IDs:
> __hsa03030 <- pathview(gene.data = genes\_change,pathway.id
updated 10.1 years ago • svlachavas
Hi,
I was trying to import the RSEM counts into DESeq2 using DESeqDataSetFromTximport function but for some reason I am getting `Error in txi$counts : $ operator is invalid for atomic vectors`. I was just following the instructions in the manual but I am getting this error. Any ideas why?
Here is the full code that...Hi,
I was trying to import the RSEM counts into DESeq2 using DESeqData…
updated 5.6 years ago • upendrakumar.devisetty
any range of samples and
assays.
the data headings from the csv are:
ID,Assay,Allele Y,Allele
X,Name,Type,Auto,Confidence,Final,Converted,Allele
Y,Allele X
where Allele Y and Allele X are the plotted values and the vectors
updated 13.6 years ago • Hans Thompson
counts_ruvseq = batch_ruv_reps$normalizedCounts # plot PCA using this matrix</pre>
groups is a vector of tissue names, counts\_deseq is a matrix of counts normalized using DESeq2's rlog function
differences is:
<pre>
[,1] [,2] [,3
updated 8.2 years ago • paul.alto
div class="preformatted">Hi,
I wonder whether there is a wild-card character in R. For example, I
use
ReadAffy("file1.txt", "file2.txt")
to read a subset of files in a directory. Can I use a wild-card...character in
this command like
ReadAffy("file*.txt") ?
Thanks a lot.
Po</div
updated 22.8 years ago • Zhao, Po
<div class="preformatted">Hello****
I am trying to use rtracklayer and specifically UCSCTableQuery to
retrieve
information from UCSC tables but I want to retrieve the information
only
on certain genomic segments. ****
** **
In the following example I try to create a UCSCTableQuery that will
return
A GRanges of the tRNAs in a set of given ranges, defined by a GRanges
object . Specificall…
updated 13.4 years ago • d r
error message:
>
> > as("myArrayLM", def);
>Error in methodsPackageMetaName("C", name) :
> 'The name of the object (e.g,. a class or generic function) to
>find in the meta-data' must be a single string (got an object
function(x){sum(width(reduce(x)))})
exonic.gene.lengths <- as.numeric(exonic.gene.sizes)
names(exonic.gene.lengths) <- names(exonic.gene.sizes)
summary(exonic.gene.lengths)
\# Min. 1st Qu. Median ...values are less than the average fragment length of 134 (for one sample). So something must be going wrong here. So the effect…
updated 7.6 years ago • Ina Hoeschele
estimateDispersions(?cds?)".?The?error?message?was:
Error?in?if?(nr?<?2)?stop("nrow(modelMatrix)?must?be?>=2.")?:
??argument?is?of?length?zero
My?input?file?is?attached.?Could?someone?let?me?know?what?the?problem?
is?
ps. the above error...Liang
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: test.txt
URL: <https: 0975235b="" 20140…
updated 11.5 years ago • 梁芳
to generate "dataset" for down-stream of DESeq2.My question is, how can I make interested column names ("i") to be recognized as a variable in design = ~i or something similar to this concept?
DEG_analysis <- function(i)
{
colData_tmp...Error in DESeqDataSet(se, design = design, ignoreRank) :
all variables in design formula must be columns in colData
updated 5.5 years ago • rekren
I'm trying to write a function that can summarize intensity matrices from Affymetrix array types that require the affy package alongside those that require the oligo package to read (incidentally, it's not clear to my why two separate packages are required to accomplish this).
The most straightforward way that I can think to do this is to pass the function three arguments: 1) the matrix of non-n…
updated 9.2 years ago • mark.aaron.fisher
<div class="preformatted">Hi,
This email is just to notify the users of lumi package and Illumina ID
mapping packages. To be better compatible with the naming convention
of
Bioconductor annotation packages, we renamed the Illumina ID mapping
packages by removing the ".db" suffix...notify the users of lumi package and Illumina ID
mapping packages. To be better compatible with the naming con…
updated 17.2 years ago • Pan Du
below
```
rawcounts <- read_csv("fibrosis_smoc2_rawcounts_unordered.csv")
# Create genotype vector
genotype <- c("smoc2_oe", "smoc2_oe", "smoc2_oe", "smoc2_oe", "smoc2_oe", "smoc2_oe", "smoc2_oe")
# Create condition vector
condition...smoc2_normal3", "smoc2_normal4")
#work around to remove geneID column that has "...1" as a name
rawcountsfixed <- rawcounts %>%
se…
updated 2.9 years ago • m-bihie
in .Call2("Integer_order4", a, b, c, d, decreasing, PACKAGE
=
"IRanges") :
'a', 'b', 'c' and 'd' must be integer vectors
This only just started happening yesterday. On machines with older
GenomicRanges/IRanges installs
updated 13.8 years ago • Tim Triche
I am trying to use ASICS for analysis of my NMR spectra.
spectra_data <- importSpectraBruker(name.dir = "C:/Spectra/NMR/Must test", sample.names = NULL, ncores = 6, ppm.grid = NULL, verbose = TRUE)
When imported, they show only 31087 points whereas all my spectra have 65536 points. I suppose it has something to do with the "ppm.grid" parameter.
It is said in the manual that is…
some issues. I hope you can help
me here..
>
> Basically, I am trying to give path view a vector with expression
values and the names of the vector has the gene names. I believe that
is what the function needs but its...not giving me the right out put.
Let me show u how:
>
> So this is the vector that we give in the vignette:
> head(gse16873.d[, 1])
> …
installed locally with the most recent version of
mySQL)
the query-functions always return empty vectors.
After looking more carefully the SQL tables we realized that by
furnishing "Probeset ID" from Affymetrix gives correct...results.
However, the function "names" used with "names(fc(pc.exonmap))[.."
returns different identifiers and the corresponding Affymetrix
"Probeset
ID" are/would...We rea…
to create a densityplot:
Error in apply(xx, 2, function(y) all(sign(diff(y)) >= 0)) :
dim(X) must have a positive length
until i finally found out that this error is thrown by the
flowCore:::findTimeChannel function...function for flowSets, since this
function will
always result in an error if there is no column named Time.
I finally realized that by calling densityplot and specifying …
<div class="preformatted">> Dear Heidi,
>
> After trying the two combinations that you talked about, just the
second
> one worked, i.e:
>
> raw1 <- readCtData(files="Prueba_Blanco001.txt", n.features=96,
n.data=96,
> column.info=list(flag=9, feature=5, type=6, Ct=7, position=1),
skip=12,
> sep="\t")
>
> the first o…
seqnames ranges strand | exp
<rle> <iranges> <rle> | <character>
[1] chr1 53947981-53947982 + | yes
[2] chr1 66585848-66585849 + | yes
[3] chr1 98738803-98738804 + | yes
[4] chr1 117456206-117456207...seqnames ranges strand | Score exp
…
updated 3.3 years ago • Marcus
0 Up NaN NaN</pre>
I think this might be due to gene names of the statistic getting stripped away inside the function by as.numeric(). Simple fix - If I make the following change...lt;- as.numeric(statistic)
G <- length(Stat)
<span style="background-color:Yellow"># ID <- names(Stat) # Replace Stat with statistic which still has names
ID &…
comes up :
```
> data <- read.FCS('data.fcs', emptyValue = TRUE)
Error: Empty keyword name detected!If it is due to the double delimiters in keyword value, please set emptyValue to FALSE and try again!)
```
Therefore...emptyValue = FALSE)
> write.FCS(data, 'data_2.fcs')
Error: Invalid input type, expected 'character' actual 'NULL'
```
I get the same error when…
updated 12 months ago • vpochic
bam file for test
> t <- scanBamHeader(bamfile)[[1]][["targets"]]
> which <- GRanges(names(t), IRanges(1, unname(t)))
>
> ##only look at chrI
> param <- ScanBamParam(which=which[1], what=character(), flag=scanBamFlag(isProperPair
updated 6.5 years ago • Jiping Wang
May
someone let me know where I could find a .CSV file that includes both
Probe
Set IDs and gene names for this array?
Thanks,
Shery</div
based on an experiment with a small number of observations the labels are quite large and only a few characters fit on the screen. As the number of observations goes up the font size goes down and more characters are printed...nbsp; I'm' wondering if I can gain control of the font size in the labels, to enable me to see more characters even in experiments based on a small number of obse…
sums : num 2 139 841 317 48 ...
# Remove all packages
> pkg = names(sessionInfo()$otherPkgs)
> pkgs = paste('package:', pkg, sep = "")
> lapply(pkgs, detach, character.only = TRUE, unload = TRUE)
require...fdef, mtable) :
unable to find an inherited method for function ‘strand’ for signature ‘"character"’
> gr …
updated 6.7 years ago • rhooads7
nor can I find a tool that can take an accession number and translate it into its organism's name. I am using R. Thank you for any help,
J. Denton
edit for clarification: for the accession number translation, an example would
updated 2.1 years ago • j_denton
QTL analysis? If, say, instead of a factor for experimental conditions, we used 0/1/2 as a numeric vector? Would DEXseq allow you to substitute a numeric vector for the condition, and would it treat this as a numeric vector
div class="preformatted">Hi All,
I use Rdbi.PgSQL, many of R scripts work with vectors
but when i query and try manipualtions on R objects
the R objects are tables and not vectors. So how does
one do this table...to vector transformatio so that my
scripts can run smoothly!!!!
Thanks in advance.
Hrishi
</div
the standard blue and pink?
Ideally I would be able to set the colour for each specific dot using a vector - in an overlay and also single datatrack!
Finally I also want to label specific data points.
Any help is very much appreciated...df2$BP+1, chromosome = chr, genome = gen, groups = factor(df2_trait,levels = c(df1_trait, df2_trait)), name="Log10P", legend=TRUE)
dtrack <- DataTrack(…
updated 7.9 years ago • p1990
Valerie Obenchain wrote:
Hi Francesco,
I changed the requirements of the varAllele argument from character to
either DNAStringSet or missing. Allowing the varAllele to be a
character
name of a metadatacolumn was problematic...an inherited method for function "predictCoding",
for signature "GRanges", "TranscriptDb", "BSgenome", "character"*
/> sessionInfo()/
/R Under development (unstabl…
Catalysis of the hydrolysis of...
... and 16774 other sets.
Item annotations:
symbol name
1302934 St8sia5 ST8 alpha-N-acetyl-neuraminide...
...
1302939 Eef1g eukaryotic translation elongat...
... and 29261 other items...the RGD IDs of my list of differentially expressed genes
from a more common gene ID.
3) Create a named list of vectors of gene identi…
It seems as though it is necessary for a column name (e.g., a channel) to match exactly the desc keyword in order for the function to work. I think a workaround would be to...It seems as though it is necessary for a column name (e.g., a channel) to match exactly the desc keyword in order for the function to work. I think a workaround would be to change the "desc" keyword in $P…
updated 11.2 years ago • erickttr
<div class="preformatted">Perfect :-)
Thank you.
-----Original Message-----
From: Gordon Smyth [mailto:smyth@wehi.edu.au]
Sent: 14 November 2004 02:36
To: bioconductor@stat.math.ethz.ch
Subject: [BioC] Confusion over limma documentation and design/contrast
matrix
>Date: Fri, 12 Nov 2004 13:42:22 -0000
>From: "michael watson (IAH-C)" <michael.watson@bbsrc.ac.uk>
>…
updated 21.1 years ago • michael watson IAH-C
<div class="preformatted">Hello,
I'd like to make clear how the 'Heat Map for Genes in Dataset' which
is one of plots in the '(project name).global.plots.pdf' and is
generated by the Gene Set Enrichment Analysis R code (GSEA.1.0.R)? The
code is available as R-GSEA...d like to make clear how the 'Heat Map for Genes in Dataset' which
is one of plots in the '(project name).global.plots.pdf' a…
updated 15.8 years ago • Radek Blatny
establish a new S4 class, based on the `` SummarizedExperiment `` class from the package of the same name.
I am wondering that the correct way of initializing a `` SummarizedExperiment `` is. The `` SummarizedExperiment `` method accepts...height:1.6">I get this error:</span></pre>
<pre>
Error in initialize(value, ...) :
invalid name for slot of class “SummarizedExperi…
updated 9.6 years ago • Thomas Sandmann
Checking samples table...
Populating samples table...
Error: Column name mismatch.
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Session info:
sessionInfo()
R version
updated 8.3 years ago • sdhutchins
gt; params <- new(
> "GOHyperGParams",
> geneIds=ipilist,
>
universeGeneIds=names(as.list(get(paste(annotation,"GO",sep="")))),
> annotation=annotation,
> ontology="BP",
> pvalueCutoff=0.001,
> conditional...testDirection = "over"
> )
> hgOver <- hyperGTest(params)
with 'ipili…
seqnames strand cigar qwidth start end width
<rle> <rle> <character> <integer> <integer> <integer> <integer>
[1] chr1 - 13S88M 101 3004617 3004704 88
[2] chr1 + 88M13S 101 3004617 3004704 88
[3] chr1...seqnames strand cigar qwidth s…
updated 6.8 years ago • James W. MacDonald
collapseTranscripts = FALSE)
Error in getBM(as.vector(featureMap), filters = names(filterValues), values = filterValues, :
The query to the BioMart webservice returned an invalid result: biomaRt expected...a character string of length 1.
Please report this on the support site at http://support.bioconductor.org
> traceback()
9: stop...The query to the BioMart webservice returned a…
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