technical replicate for each condition
and, according to the user guide provided by Simon Anders, we must sum
up their counts to get a single column corresponding to a unique
biological replicate. At the end I end up with two...to estimate the
dispersion of the normalized counts... an error message appears
indicating that "X must be an array of at least two dimensions". I
attach my results and th…
Order by: Relevance
bioconductor@r-project.org>
Sent: Wednesday, November 30, 2011 4:00 PM
Subject: Re: [BioC] Probe level normalization
Hi Suresh,
On 11/30/2011 7:49 AM, suri ghani wrote:
> How to perform the normalization using the individual
updated 14.0 years ago • suri ghani
Can I set the position of the name of the chromosome when using an IdeogramTrack?
This code:
<pre>
transcriptID <- "ENST00000421310"
chromosome <- "chr6"
genome...http://s18.postimg.org/n9eliaf9l/show.png" style="height:250px; width:574px"/>
* I would like the name of the chromosome to be placed above the chromosome, like the transcript name is placed above the tran…
updated 9.7 years ago • stianlagstad
When I learn the package minfi, I meet the error. It occurs when I generate mapToGenome using demo data MsetEx.
<pre>
>library("minfi")
>library("minfiData")
</pre>
<pre>
> my.GMsetEx<-mapToGenome(MsetEx)
Error in checkSlotAssignment(object, name, value) :
assignment of an object of class “GRanges” is not valid for slot ‘rowRanges’ in a…
Hi BioC community,
I have proteomics data with a multi-level experiment design, of the same type of the one described at paragraph 8.7 in limma user’s guide :
* I have 7 patients in Condition...than the one in the user's guide
>design <- model.matrix(~0+Treat)
> colnames(design) <- levels(Treat)
> corfit <- duplicateCorrelation(eset,des…
updated 10.2 years ago • eleonoregravier
Dear bioconductors
Must be a very basic question but I'm unable to find how to generate an order ranked genelist to feed into gseKEGG function...Dear bioconductors
Must be a very basic question but I'm unable to find how to generate an order ranked genelist to feed into gseKEGG function in...ClusterProfiler.
I work on R and have a dataframe or matrix of gene names with associated FC values, pv…
updated 8.3 years ago • bruno.saubamea
Hi,
it would be nice if the first factor can be names differently than 'condition'. It is really hard to figure out that this needs to be specified and even that it is case-sensitive
updated 9.0 years ago • bjoern.gruening
genomics and multi-omics data sets of Atlantic salmon.
**Competence**
The successful applicant must meet the conditions defined for admission to a PhD programme at NMBU. The applicant must have an academically relevant...corresponding to a five-year Norwegian degree programme, where 120 credits are at master's degree level. The applicant must have a documented strong academic background in g…
updated 4.4 years ago • marie
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060925/
07901446/attachment.pl</div
updated 19.2 years ago • Bing Zhang
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20071023/
3ea36b11/attachment.pl</div
updated 18.1 years ago • li lilingdu
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070619/
df591863/attachment.pl</div
updated 18.5 years ago • Steven Wanyee
error
"Error in ViSEAGO::Custom2GO("C:/Users/folder/Downloads/goa_file_untrimmed.csv") :
GOID must be a valid identifiant. see select(GO.db,columns=columns(GO.db),keys=keys(GO.db)"
## connect to Custom file that has been trimmed
updated 4.4 years ago • jabbar_campbell
Dear Community,
based on a validation project of mutational signatures, a microarray expression dataset from GEO was processed, in order to evaluate...storageMode: lockedEnvironment)
assayData: 284258 features, 76 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM1887886 GSM1887887 ... GSM1887961 (76 total)
varLabels: title geo_acce…
updated 5.7 years ago • svlachavas
I have two granges objects that I want to overlap based on the metadata column gene names - I essentially want to find the ranges that correlate to the same gene names between the two sets. Can anyone help me with
updated 4.4 years ago • grr4006
preformatted">Hi, there;
I am new to bioconductor, thus I have a simple question.
How to get gene names in arabidopsis array, I can get affyID, but hope
to
get gene name or find affyID for a list of genes. I tried
> getSYMBOL("267139_s_at
updated 21.2 years ago • Fangxin Hong
in GEO.
I made a strange observation while cutting the cohort in two based on a median expression level for each probe: for several probes the cohort was not divided in 2 sub groups with equal number of patients as it should...be. For example the cohort was divided in 30% of patients below and 70% above the median expression level of probe "212970\_at". I found out that for many patients the exp…
updated 8.7 years ago • Amos Kirilovsky
<div class="preformatted">Hi,
I realized that subsetting an IntegerList object (and probably other
IRanges list objects) by the list names plus replacing list element
values behaves unexpectedly (at least for me) when the list is not
sorted by its element's...realized that subsetting an IntegerList object (and probably other
IRanges list objects) by the list names plus replacing list eleme…
updated 14.1 years ago • Manuela Hummel
and GRangesList subject) by limiting the search to ranges in query and subject that have the same name?
To be more concrete, I have
1. a GRangesList, where every (uniquely named) element corresponds to a transcript CDS, and
2. a GRangesList...with named elements corresponding to multiple transcript 3’UTR (per CDS).
I would like to select those elements from list (2.) that...closest to the …
updated 9.8 years ago • Maurits
Hello,everyone! We know that beadarray can handle bead-level data, but it seems that there is no way for lumi to do this.
lumi could read 'summarized intensities' in, just as follows:
<pre...white-space:normal">
</span></font>
</pre>
but no way to read in this directly:
<pre>
#a bead-level text file for one sample, contains 'array_address_id intensity locX loc…
updated 9.7 years ago • gnilihzeux
When I run
"arrayQualityMetrics" to the background corrected (RMA) and normalized
(quantiles) probe-level data (thus processing the non-summarized
AffyBatch object) I get a PCA showing two distinct groups (not a
random separation
every probesets, between 2,15 and 14,6
(mean=
5,78).
What value should I set to minimum expression level?
For Affymetrix experiments, the default here has been set at log2(10),
but
I think it seems very stringent to my data, what
updated 17.9 years ago • Patrícia Luiza Nunes da Costa
fluids, plant, or animal tissues, etc.). This will involve intensive effort in assay development and validation.
• Operate and oversee operation of the Facility’s analytical equipment. Key instrumentation currently includes...at https://jobs.illinois.edu, directly apply to our position and upload cover letter, resume, and names/contact information for three references by April 6, 2022. Online ap…
updated 3.7 years ago • Jenny Drnevich
div class="preformatted">Hello,
I read the limma user guide on the topics of multi-level experiments
and found the information very useful. But my design is a little more
complicated, and I would like to consult...and set contrasts
normal-tumorPos for (2) and normal-tumorNeg for (3). Or I should
follow the multi-level design instructions to include the type_AR and
chip in the design (paste th…
method = "glmLRT",
+ paired=FALSE)
And it gives: "Errore in names(x) <- value : l'attributo 'names' [7] dev'essere della stessa lunghezza del vettore [1]" .
I suppose that the two vectors "dataSmNT_short.miR
updated 4.0 years ago • Gandino
in validObject(.Object) :
invalid class “SummarizedExperiment” object: 1: invalid object for slot "NAMES" in class "SummarizedExperiment": got class "array", should be or extend class "characterORNULL"
invalid class “SummarizedExperiment...object: 2: 'names(x)' must be NULL or a character vector with no attributes
</pre>
I use this code:
<pre>
txi.kallisto <- tximport(s…
updated 8.2 years ago • jarod_v6@libero.it
exonsBy(hgTxDb, 'tx')
That the object returned (eTx in this case) doesn't contain the
transcript names. But if we use
e <- exonsBy(hgTxDb, 'gene')
The ensembl gene names are returned as the names of GRangesList "e".
I'm wondering if...there's a convenient way of annotating the eTx object
with the transcript names also?
Thanks,
Paul.
--
Paul Geeleher (PhD Student)
School of Mathematic…
updated 14.9 years ago • Paul Geeleher
dds <- DESeq(dds)
> res <- results(dds, tidy=TRUE)
Error in checkSlotAssignment(object, name, value) :
assignment of an object of class “DFrame” is not valid for slot ‘elementMetadata’ in an object of class “DESeqResults
updated 4.8 years ago • james
Hello,
I was doing normalization step in R but it is showing me this error..
```
>names=dir(pattern="CEL.gz")
> My_CELdata=ReadAffy(widget=TRUE)
Error: cannot allocate vector of size 2.6 Gb
> My_CELdata=ReadAffy...widget=TRUE)
Error: the following are not valid files:
C:/users/bioproject1/Desktop/RAW_DATA$
> My_CELdata=ReadAffy(widget=TRUE)
Error in if…
updated 5.8 years ago • manuchandwadkar
preformatted">Hi,
I am approaching beadarray for the first time and I have a query about
the bead-level data that I have received. From what I read four
columns are expected in the .txt files (Code, Grn, GnrX, GnrY). I
want to clarify
to join Affymetrix U133A and
B
arrays. The rownames of the expression matrix are set to the probe
names. To do this I want to treat all the probe names that are shared
between the arrays as unique by appending an "_A" or "_B". I do this...by
finding the names of the probe that are shared and then running:
rownames(expr.matrix[match(ProbeIntersect,rownames(expr.matrix)),]) <..._A",sep=""…
analysis, keeping the original identifiers, appended with a number/letter, to give a unique name to each disambiguated sequence. I have been playing with DECIPHER's DB2Seqs function, but I don't seem to understand the...Error in DB2Seqs(file = "", stringset_10k_disambig, tblName = "disambig10k.fasta") : 'dbFile' must be a character string or SQLiteConnection.
DB2Seqs(getwd(), stringset_10k…
updated 5.5 years ago • joannew
mutated
6. cancer_subtype4 wildtype
Few things of note:
1.**Total cancer subtypes**: 6(levels)
2.Each subtype considered has both mutated and wild type representation.
3.The number of wild type is more within...can have 3 samples with wild type genotype and only 1 of that mutated.
4.**Number of levels of mutation_status**: 2 (wildtype and mutant)
My design is as f…
modules_names, col = module2colors_colors)
)
cell_type_legend <- Legend(
labels = names(celltype2colors), # Cell type names
legend_gp = gpar(fill = celltype2colors), # Corresponding colors
title = "Cell Type"
)
cell_subtype_legend...lt;- Legend(
labels = names(cellsubtype2colors), # Cell subtype names
legend_gp = gpar(fill = cellsubtype2colors), # Corresponding c…
updated 13 months ago • nromerov
read count. after I get them, how can I reach to the gene I want? because it wont give me the every name of the gene, right?
would be great if you can help me
updated 2.1 years ago • Gülsüm
plot question I am afraid. Thanks for all the help with the
previous one.
I have the expression levels of a number of exons in a gene. I would
look like to see how the expression levels vary across the gene. For
each of the exons...I have a start position and a stop position.
It is easy enough to plot the expression level verses the start/stop
position:
> plot(exonAnnot[rownames(temp),…
Hi -
I am using DESEq2 to analyze a dataset with two factors, each with two levels. I am therefore using a standard model matrix, with the following formula and output from resultsNames(des):
<pre>
> des...c('nutrients','yes','no'))</pre>
And the same for the 'snail' treatment, with the argument
<pre>
name='nutrientsyes.snailyes'</pre>
for the interaction.&am…
updated 10.2 years ago • ryan.mcminds
div class="preformatted">
Hi,
I have a situation where I have a vector of variable names. If I call
any of them, I get a text string (the name is surrounded by ""). How
can I use that as a variable name again?
For instance...1], because
that only shows "a"...
Is there a simple way to indicate that "a" should be taken as the name
of an object, and not as a string? If so, I haven't found it...…
updated 18.8 years ago • J.delasHeras@ed.ac.uk
treatments, I have created a heatmap with the geneIDs but I am struggling to find a way to add gene names or alternatively produce a list of gene names that are deferentially expressed. I have a GFF3 file and a cds file for the
updated 2.8 years ago • Chelsea
I have a huge list of gene names, and I'd like to map corresponding gene IDs to each name. I've tried using this R library: `` org.Hs.eg.db ``, but it creates...more IDs than names, making it hard to map the results together, especially if the list is long.
Example of an input file (7 gene names):
RPS6KB2...read input file
GeneCol = as.character(input$Gene.name) #a…
updated 7.4 years ago • Bayram Sarilmaz
Invalid attribute(s): coding
Please use the function 'listAttributes' to get valid attribute names
```
I ran the same code ~2 years ago and it worked fine. I've explored other Attributes via the "listAttributes...function to see if the attribute name for coding sequence has been updated but I can't see to find anything close.
Note that I'm using an archived version of ensembl
updated 2.2 years ago • andrew.b.kleist
mildly updated; new HTML vignette on working with the ontology
- EMBL-EBI recased all field names to upper case; code using field names must be modified
updated 10.3 years ago • Vincent J. Carey, Jr.
Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
Problematic argument:
..1 = Inf
Did you misspell an argument name?
Run `rlang::last_trace()` to see where the error occurred
tell me where I could find
the correct version of rgu34a package for R2.1.0?
atab <- aafTableAnn( Names, "rgu34a", aaf.handler() )
[1] "You have package rgu34a but the incorrect version"
Note: http://www.bioconductor.org/data/metaData...does not seem to have
a valid repository, skipping
Warning message:
Failed to read replisting at http://www.bioconductor.org/data/metaData
in: getReplisti…
updated 20.6 years ago • Yanqin Yang
data.frame': 5016 obs. of 4 variables:
$ Genes : Factor w/ 264 levels "ABHD5","ACOT4",..: 1 2 3 4 5 6 7 8 9 10 ...
$ Timepoints: num 1 1 1 1 1 1 1 1 1 1 ...
$ value : num -2.05 -8.36 -2.06 -3.84 -6.59 ...
$ X20 : Factor w/ 66 levels "M10.1...M10.2",..: 53 59 53 53 44 6 29 12 29 19 ...
..- attr(*, "names")= chr "ABHD5" "ACOT4" "ACTN4" "ACTR10" ...
…
updated 6.0 years ago • mohammedtoufiq91
version number for a particular BioC version.
I know all\_group() will return the list of package names, but I also need the versions. Where can I get these from?
Cheers,
Nathan
updated 9.8 years ago • nathan.watsonhaigh
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20071130/
c91a8e11/attachment.pl</div
updated 18.0 years ago • zhi.zhang@syngenta.com
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060220/
83fa0003/attachment.pl</div
updated 19.8 years ago • Talloen, Willem [PRDBE]
c('6233')
#Transcriptdb
txdb19 = TxDb.Hsapiens.UCSC.hg19.knownGene
#SNPs - renamed seq levels to be compatible with txdb
snps = getSNPlocs(c("ch1","ch2"),as.GRanges=T)
renamed.levels = gsub("ch","chr",seqlevels(snps))
names...call gives this error:
Error in .setSeqNames(x, value) :
The replacement value for isActiveSeq must be a logical vector,
with
names that match the seqlevels of the o…
updated 13.8 years ago • Alex Gutteridge
of two types, one or more vignettes and a reference manual; and they
have the same file name, PackageName.pdf. When downloaded some file
name manipulation is required, or accept PackageName(1).pdf.
I suggest the...documents be given different names, for example the
reference manual could be named PackageNameRefMan.pdf. Package
checking could enforce the rule.
-- output
updated 11.3 years ago • Guest User
Hi,
Is there an option to keep the original file name when adding a 'web' file by `bfcadd`?
For example,
```
bfc0 <- BiocFileCache(tempdir(), ask = F)
add1 <- bfcadd(bfc0, "bwa",
fpath = "https://raw.githubusercontent.com...tl_bwa.R"))
add1
## "/tmp/RtmpzSEpeG/b01175a39e7e_tl_bwa.R"
```
A prefix was added to the file name. Is it possible to keep the ori…
updated 5.8 years ago • Qiang
mart, dataset = dataset, verbose = verbose) :
The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets function.</pre>
However, if i repeatedly enter that line
updated 7.8 years ago • Brian Gudenas
Invalid attribute(s): refseq_dna
Please use the function 'listAttributes' to get valid attribute names
What attributes should I use to instead "refseq_dna"?
Yours sincerely,
Jianhong Ou
jianhong.ou at umassmed.edu
vcf, txdb,
seqSource=Athaliana)"
to detect coding SNPs. The problem is that the chromosome names are
not
consistent among VCF, txdb and BSgenome. In vcf, the chromosome name
is
"Chr*", in txdb, the chr name is "Chr", but in BSgenome...the chr name
is
"chr*" .
I know I can use renameSeqlevels() to adjust the seqlevels (chromosome
names) of the VCF object to match that of the...txdb annotation. Bu…
updated 13.2 years ago • sun
because it looks here as the technical
>replicates are included in the targets file (on the same level as the
>biological replicates) and should therefore also be included in a
>following contrast matrix. But the contrast.matrix...gt;
>Another question that was not aswered is how to treat different
replicates
>on different levels. Since I have 1-2 biopsy taken f…
been
representing as GRanges, and
(b) I'd like the underlying code to be smart and match chromosome
names up in the RleList and the GRanges object (not rely on
chromosomes being ordered the same in the two objects), and
(c) I'd like...myRegions)
# Error in RleViewsList(rleList = subject, rangesList = start) :
# 'rangesList' must be a RangesList object
## can't use a simple coercion
Views( myRl…
updated 14.3 years ago • Janet Young
Amoxicillin + Carbon_Source:Amoxicillin)
dds$Carbon_Source = factor(dds$Carbon_Source, levels=c("glucose", "dextrin"))
dds$Time_Point = factor(dds$Time_Point, levels=c("T0", "T1", "T2"))
dds$Amoxicillin = factor(dds$Amoxicillin, levels...of amoxicillin different depending on glucose vs dextrin? (across timepoints)
res1 = results(DDS, name = "Carbon_Sourcedextrin.Amoxicillinamox")
#The ef…
genes,
>>>
>>> now the problem is that how can i convert the probe ID's to Gene
names
>>> using annotation package and with what database because there is
no
>>> database in bioconductor related...to t. gondii.
>>>
>>> if i have to pick these gene names from NCBI then how …
updated 14.9 years ago • Paul Geeleher
advice about where i am going wrong with a loop i'm trying to write for cleaning up UNIPROT data names.
Basically, the name i have from proteomics analysis is something like tr|A0A02DLI66|A0A02DLI66\_MYTGA but i would
updated 7.2 years ago • laural710
in `collect()`:
! Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
Problematic argument:
..1 = Inf
Did you misspell an argument name?
Run `rlang::last_trace()` to see where the error occurred
updated 22 months ago • goldenboy
in `collect()`:
! Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
x Problematic argument:
. ..1 = Inf
i Did you misspell an argument name
Recent ...
Replies
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 …
Comment: problem reading bam files into nucleR
by
efoss
▴
10
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
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
•
0
Thank you very much! will take that into consideration
Awards
• All
Commentator to
sina.nassiri
▴
130
Popular Question to
Hervé Pagès
16k
Popular Question to
jared.andrews07
▴
30
Popular Question to
shepherl
4.2k
Locations
• All
St Louis, MO, 21 minutes ago
United Kingdom, 21 minutes ago
The city by the bay, 24 minutes ago
United States, 27 minutes ago
Pakistan, 1 hour ago
St Louis, MO, 21 minutes ago
United Kingdom, 21 minutes ago
The city by the bay, 24 minutes ago
United States, 27 minutes ago
Pakistan, 1 hour ago
Traffic: 634 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6