sample_meta$sampleID)
sample_meta$Group <- as.factor(sample_meta$Group)
sample_meta$Name <- as.factor(sample_meta$Name)
#get the clusterID from fSOM object
clusterID <- as.factor(fSOM$FlowSOM$map$mapping[,1...levels(clusterID) <- fSOM$metaclustering
#I need to have a list of "file name" "from" "to". The original one from here ht…
Order by: Relevance
Calling frames...Error in findInterval(spl27.f\[\[ii\]\], splfr0e\[\[ii\]\]) :
'vec' must be sorted non-decreasingly and not contain NAs
In addition: Warning messages:
1: In \`levels<-\`(\`\*tmp\*\`, value = if (nl == nL) as.character...labels) else paste0(labels, :
duplicated levels in factors are deprecated
2: In \`levels<-\…
updated 9.7 years ago • alper.celik
I'm interested in plotting the exon usage as it's done in the plotDEXSeq function but at sample level. Is it really possible? How could I do it?
Best,
<span style="line-height:1.6">Xavier</span
updated 10.7 years ago • Xavier Pastor
div class="preformatted">Hi everyone,
Does anyone know how to go from gene name to ENSEMBL ID?
I'm using lumi to analyze my microarray data, however the names get
changed from NuID to gene name when reading
updated 12.1 years ago • Kripa R
After obtaining the gene-level expression for the CCLE project using `recount3`, I am trying to obtain the transcript-level data.
As far as I can tell this...After obtaining the gene-level expression for the CCLE project using `recount3`, I am trying to obtain the transcript-level data.
As far as I can tell this is not possible with `recount3` but it should be possible with `recount`:
``…
<div class="preformatted">On Fri, May 30, 2003 at 05:28:45PM +0100, Crispin Miller wrote:
> Hi,
> Just a quick question about low expression levels on Affy systems -
I hope it's not too off-topic; it is about normalisation and data
analysis...
> I've heard a lot of people advocating...at 05:28:45PM +0100, Crispin Miller wrote:
> Hi,
> Just a quick question…
seq data from TCGA using edgeR. The results of differential expression analysis has NAs under Gene names and Gene symbols. The EntrezID corresponding to it doesn't give a valid Gene name. What could be wrong? The following command
updated 5.7 years ago • fawazfebin
Could you add selected row names to a ```pheatmap``` instead of including them all using ```show_rownames = T```?
Something similar was asked few years ago here https...10, show_colnames = F, show_rownames = labgenes, color = colorRampPalette(rev(brewer.pal(n = 7, name ="RdYlBu")))(100
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070831/
05abf0aa/attachment.pl</div
updated 18.3 years ago • Roger Liu
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070904/
c4f35be0/attachment.pl</div
updated 18.3 years ago • martin.schumacher@novartis.com
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080330/
acd6aaff/attachment.pl</div
updated 17.7 years ago • Kathy Duncan
div class="preformatted">Deal All,
Anybody knows that how to set the significance level, such as 0.01,
0.05, after I got the icc.agreement? Thank you.
Xin LIU
This e-mail is from ArraDx Ltd
The e-mail and any files
updated 21.1 years ago • Liu, Xin
problem.
I performed hierarchical clustering on a filtered sample (cv=0.04, at
least 2 samples > level of log 9) of 80 tumor samples, and obtained
several groups. Some of these clusters were definitely more stable
than
others...analysis
using PAMR to obtain a gene list. However, the misclassification rate
during cross-validation for my good prognosis is fairly low and stable
(<0.05…
updated 21.5 years ago • Tan, MinHan
metadata information for each library (meta). One of my metadata columns is a factor with 5 levels (factors). I want to do all pairwise comparisons for all 5 factor levels.
I've tried to do it this way:
dds = DESeqDataSetFromMatrix...in the otu table, but I get an error:
Error in FUN(X\[\[i\]\], ...) : assay colnames() must be NULL or equal c…
updated 8.8 years ago • natalie.hull
Hi,
Getting an unexpected error with DESeq2.
> dds = DESeq(dds)
using pre-existing normalization factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 792 genes
-- DESeq argument 'minReplicatesForRep…
updated 7.1 years ago • ashley.doane
of the columns in the beta matrix will affect the cpg sites finally found. When I matched the column names of the beta matrix identical with the row names of the PD files, I even got the 'Error: ChAMP.DMP Have not detected even one...to Compare : 1, 3
Contrast Matrix
Contrasts
Levels p3-p1
p1 -1
p3 1
You have found 802 significant MVPs with a BH adjusted P-value bel…
updated 4.3 years ago • Jinyue
div class="preformatted">Hi,
I am having problems in finding the marker names in a flowFrame.
(The marker names mapped onto the channel names - i.e.FL1-H, FL2-H,
FL3-H
and FL4-H).
I wrote the code:
FCS <- read.FCS...subfilesdir2)
FCS
featureNames(FCS)
and got this output - but it does not seem to show any new names (i.e
CD45),
so am I doing the right thing:
flowFrame object 'P:/Pro…
updated 17.5 years ago • Anne
am not sure whether it means "cryptocephal" or "Calreticulin".
I found a description that the gene name of drosophila starts with lowercase if named for recessive mutant and uppercase if named for dominant mutant. But it...to tell when I searched the homepage...
Is there any good way to detect the correct official full name? Or is there any way to get an annotated file with both gene symbol a…
updated 3.6 years ago • Chise
question is with regards to groupGO function. I was wondering what would be a good value to use for "level" attribute in the function. Or is there a way to arrive at the most optimal value for the attribute "level".
thanks
ggo...groupGO(gene = as.character(subset\_aggdf$annot.gene\_id),
OrgDb = org.Mm.eg.db,
ont = "MF",
level = 10,
readable = TRUE
updated 7.6 years ago • saadmurtazakhan
Error in parse_pd_for_read_fs(files, path, pattern, phenoData, sep, as.is, :
Argument 'phenoData' must be of type 'AnnotatedDataFrame' or a filename
of a text file containing the phenotypic information
```
As I do not know much
updated 5.1 years ago • Rainer
How to get gene names for the probe id's using
<pre>
pd.hta.2.0?</pre
updated 7.2 years ago • sunandinisharma
CEL files. I have the expression values and
the colnames extracted as matrix files. The colnames
are named with the .cel file names. Now in a different
file the .CEL files are referenced to sample name. I
am interested in classifying...I can
define certain files (as patterns) as one go and
classiffy them as some category. The file names are
unique with numbers and doe not seem to have specific
p…
for the prostate cancer, and have managed to extract the counts using assay(). The column names of the dataframe extracted however, whilst they look like identifiers, bear no resemblance to any identifiers in the...TCGA database.
I have a separate download of clinical data, with TCGA identifiers and sample names for the same data set. How does one link up columns in the assay with known sample n…
updated 8.3 years ago • b.curran
with no own content or logic
(maintained Steffen Durinck in sunny Berkeley.)
Questions at levels 2 and 3 are good to ask on this list and are
usually
efficiently answered e.g. by Steffen or Rhoda.
What you report is, afaIct...an Ensembl data content problem, i.e.
level
1. Here the advise is to email the Ensembl help desk: helpdesk at
ensembl.org
I hope this helps, please let us know if you...i…
updated 16.8 years ago • Wolfgang Huber
Hello,
I am working with RNA Seq samples from an experiment similar to that described in section 9.7 of the limma user guide (multi-level experiments). The difference is that we have multiple fastq files per subject per condition per tissue. For example:
File01a...samples from an experiment similar to that described in section 9.7 of the limma user guide (multi-level experiments). The diff…
updated 6.6 years ago • richard.vinisko
comparisons that are 0s compared to maybe 2 samples with counts when comparing between a treatment (named BOTH) group of 6 and group of 6 control (named CLEAN). ![picture of results][1]
Is it valid to use these genes where maybe 2 samples
in the chemistry/instrumentation is enough to be a
rather large component of variance) and has three levels. By three
levels, I mean there are 2 different treatments and 1 control. When I
push the workflow through, everything works...fine, but I'm having a
hard
time delineating which level is responsible for a gene being
identified
as significantly differentially expressed. I understand that (i…
updated 13.6 years ago • Ingrid Lindquist
Hello,
I performed an analysis of differential expression with SAM method, obtaining the genes that are up and down. I used these scripts:
<pre>
> samfit = SAM(exprdc, group, resp.type="Two class unpaired", fdr.output=.01)</pre>
<pre>
> sigSAM_low = as.numeric(samfit$siggenes.table$genes.lo[ ,2])</pre>
<pre>
> sigSAM_up = as.nume…
updated 10.3 years ago • santi.cabellos
<div class="preformatted">Dear BioC,
How can I install all metaData available (including
CDF,Probe and Annotation) information from URL:
http://www.bioconductor.org/packages/data/annotation/stable/src/contri
b/html/
I am doing follwoing, and I get all latest results
from that URL. But somehow , I get error msg. as shown
below. Please, help me if someone have done this
before or point me…
<div class="preformatted">
I'm trying to use edgeR to analyse RNA-seq data following the guidance
of "edgeR: differential expression analysis of digital gene expression
data".
I have done exactly as the manual told and when tapping the command "d
<-
DGEList(counts=d, group=group)", then an error comes as
"?????????DGEList(counts = d, group = group) :
Length of 'group' must equal nu…
equal weight to each species. My first approach was to use species group by tissue as the design levels:
```r
> design.Option1 <- model.matrix(~ 0 + ExSamples$Option1)
> colnames(design.Option1) <- levels(ExSamples$Option1...gt; design.Option2 <- model.matrix( ~ 0 + ExSamples$Option2)
> colnames(design.Option2) <- levels(ExSamples$Option2)
…
updated 4.5 years ago • David
Invalid attribute(s): external_gene_name
Please use the function 'listAttributes' to get valid attribute names
I am trying to use the attribute external_gene_name but it doesn't recognize the attribute when it
div class="preformatted">hi,
when i have tried to load a package from local zip file named
"knnTree"?
I get an error messages Like:
'knnTree' is not a valid package -- installed < 2.0.0?
and
"couldn't find function "knn.var
updated 21.2 years ago • Nebahat Noyan
with the baseMean, log2 fold change, and pvalues, except that the rows are numbered rather than named by gene.
I would assume that the genes are listed in the same order that they appeared in the countData, ie I could annotate...the results file with gene names by simply assigning it the countData row names. I hesitate to do this, however, in case some other ordering occurred
updated 8.4 years ago • kalaga
cnts, samp, ~ cond)
dds <- DESeq(dds)
dds$cond
# [1] a a a a a b b b b b
# Levels: a b
## works
res <- results(dds, c("cond", "a", "b"))
dds$cond <- factor(dds$cond, levels = c("b","a"))
dds$cond
# [1] a a a a a b b b b b
#Levels: b a
# Error
results...object, contrast, expanded = isExpanded, listValues = listValues, :
as b is the reference level, was…
updated 8.1 years ago • Chris Stubben
I have a sample dataset derived from single cell RNA Sequencing with 1800 samples. Some genes have only few counts. Using WGCNA I can compute modules and even define the module membership for each gene for each module. I want to find the number of counts for which a gene would be safely clustered into one (or 2) module(s).
Would it be valid to: Define genes with counts e.g. lower 5, by computing…
updated 8.4 years ago • ly.leifels
results in excel, the column header was missing on the final
column. The column header for probset name was actually the name of
the first array. When I normalized using RMAexpress, I could see that
the problem was that the probset...name was missing and all the names of
the arrays were shifted to the left. Should I simply insert the
probeset column header
updated 22.4 years ago • Haddad, Ramsi
nbsp;
Hi all,
I'm trying to find the names (e.g. SYMBOLS) corresponding to gene ID using the "org.Dm.eg.db" and "TxDb.Dmelanogaster.UCSC.dm3.ensGene" libraries...error:
<pre>
Error in .testForValidKeys(x, keys, keytype) :
None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to see a listing of valid arguments.</pre>
However, when I try …
updated 10.6 years ago • Patrick Schorderet
I can provide these information
by
pasting a list of identifiers, so the requested information must be
somewhere in the tables.
My found solution is kind of indirect by first getting a table of all
UCSC names together with...gene symbols, finding the corresponding UCSC
names to my symbols and then searching these UCSC names in a table of
all UCSC names with location.
Thank you in advance,
Chris…
updated 16.4 years ago • Christian Ruckert
comparing polyploids to diploids for differential gene expression, what is the effect of polyploidy level on RUVs normalisation ?
If anyone has a clear and possibly detailed explanation that would be much appreciated :D
Thanks
updated 9.6 years ago • thomas.wolfe
unique positions per strand for scaffold_3
Calculating shift for scaffold_3
100Error in names(res) <- nms :
'names' attribute [4] must be the same length as the vector [2]
In addition: Warning message:
stop worker failed:
'clear_cluster
updated 7.3 years ago • gavrielmatt
Hi,
Does anyone know how to contrast only a single pair of conditions in JunctionSeq (which is based on DEXseq AFAIK), if there are > 2 levels of the condition? I would like to test the null hypothesis that there is no condition:bin effect between one pair of conditions...a single pair of conditions in JunctionSeq (which is based on DEXseq AFAIK), if there are > 2 levels of the con…
updated 9.1 years ago • stuart
preformatted">Hi,
I get "Error in sqliteExecStatement(con, statement, bind.data) : ,
bind.data must have non-zero dimensions" when run.
It seems similar this error
https://stat.ethz.ch/pipermail/bioconductor/2011-February...ndf", full.names =
TRUE)
####################################################
## Make info package MUST have only one POS and ##
## NDF file in the directory …
updated 13.8 years ago • mabawsa
gene_association.tair") :
At least one DB object ID has multiple DB object symbols or names in gene ontology annotation file.
In addition: Warning messages:
1: In result_fetch(res@ptr, n = n) :
SQL statements must be issued...of dbGetQuery() or dbSendQuery().
2: In result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement…
div class="preformatted">Hello,
The latest version of arrayQualityMetrics names the arrays "1, 2,
3...".
How do I know which number corresponds to which .cel file? In previous
versions the name was the .cel file...name. Why the change?
---
Dr. Ricardo A. Ch?vez Montes
Laboratorio Nacional de Genomica para la Biodiversidad
CINVESTAV-IPN
Km. 9.6
updated 14.2 years ago • rchavez
gt; colnames( counts ) <- paste(c(rep("Gene.ID",1),rep("Reads.Count",1)),sep=",") \# sample names
Error in \`colnames<-\`(\`\*tmp\*\`, value = c("Gene.ID", "Reads.Count")) :
'names' attribute \[2\] must be the same length as the vector
updated 9.5 years ago • t3h096
in
the results of DESeq2 analysis really mean for the interaction of a
two-factor two-level design? Is it possible to compare 'Factor A
level 1' to ' Factor A level 2' or other similar comparison?
Here are the part of codes...phyloseq.obj, design=~ Treatment*Day)
colData(dds)$Treatment<-
factor(colData(dds)$Treatment,levels=c("Control","Treat"));
colData(dds)$Day<- factor(colDat…
infection). To make it easier, I created a variable of the grouping of two variables:
<pre>
levels(dds$group)
[1] "treated_Inf" "treated_NonInf" "untreated_Inf" "untreated_NonInf"</pre>
What I understand from the pipeline...to get the right variables to compare
<pre>
dds$group<-relevel(dds$group,ref="untreated_NonInf")
levels(dds$group)
[1] "untreated_No…
updated 7.3 years ago • andrebolerbarros
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070409/
bafd51cd/attachment.pl</div
updated 18.7 years ago • Lana Schaffer
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20071126/
1d89aece/attachment.pl</div
updated 18.0 years ago • Ingrid H. G. Østensen
Hi,
I conducted a multi-level experiment with gene expression measures in multiple brain regions in 2 groups.
So for instance, my **data** for region...Hi,
I conducted a multi-level experiment with gene expression measures in multiple brain regions in 2 groups.
So for instance, my **data** for region 1...look like this (note that for this post, I renamed the rows: these are gene names in …
updated 5.8 years ago • s.vander.sluis
metadata info please help me is it a bug or I am doing anything wrong even though i have same number names as columns still getting a error
Thank you
```
tpm_count <- read.table("TPM.tsv", sep="\t", header=T, row.names=1)
dim(tpm_count...tpm_count), colData=DataFrame(label=cell.labels)
)
)
**Error in method(object) : all assays must have the same nrow and ncol**
sessionInfo( )
R ve…
updated 3.7 years ago • Lucky
RNA-Seq analyses. In Amplicon
sequencing, is there any package/function which can extract amplicon-
level
read counts and GC content from an aligned file of BAM format? The
same
question to exon-level read counts and GC content
updated 13.5 years ago • Yu Chuan Tai
on kallisto aligned data from the TOIL project. I want to use `tximport` to summarize the transcript level data to the gene level. The format of the abundance and count files is a matrix with ENST transcript IDs as rows and sample...names as columns. I am wondering how I can use `tximport` to summarize these transcripts to the gene level given that the data...format. If it is not possible to use …
error message:
"Error in asMethod(object) : all the ranges in the object to coerce to GPos must have a width of 1"
Can someone help us understanding where is our error, and how to correct it ?
Here is the code:
library(CAGEfightR...ix]
rownames <- str_extract(sampnames, "W|H")
design <- data.frame(row.names = sampnames, Name = sampnames, BigWigPlus = bw_plus, BigWigMin…
updated 6.6 years ago • July
strong written and verbal communication skills. He/she must have a minimum of five years of relevant experience in data science, and demonstrate experience with algorithms for...as application of advanced data analytics, including data mining and visualization. The incumbent must demonstrate deep understanding of database design and structure. Experience should include work with applications...ba…
updated 9.1 years ago • kaufmanm
I have a data set where samples are grouped according to their health status (3 levels) and sampling timepoints (2 levels for each sample). This would be a simplified version of the data set:
<pre>
df <- data.frame...I have a data set where samples are grouped according to their health status (3 levels) and sampling timepoints (2 levels for each sample). This would be a simplified …
updated 8.0 years ago • serpalma.v
and i
am ending up with following error.
Cy3.norm <-
apply(cy3.channel,2,function(v){tapply(v,names(v),function(x){median(x
,na.rm=TRUE)})})
Error in tapply(v, names(v), function(x) { :
arguments must have same length
any help is appreciated
Since the latest FlowCore update, when I try to rename the $PnS parameters those marker names are not saved to my file when writing FCS files. However, when I rename $PnN parameters the marker names do get saved to file
updated 4.7 years ago • jasonemo
Recent ...
Replies
Comment: How can I correctly use phyloseq with Docker?
by
Suzy
•
0
The graphics in [Snow Rider][1] are colorful and charming, adding to the festive atmosphere.
[1]: https://snowriderio.io
Comment: GOseq Probability Weight Function bad fit
by
ejasge.r.m
•
0
When performing GO analysis with GOseq, i s important to carefully check your input and assumptions, just like reviewing choices on the McD…
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…
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
United States, 30 minutes ago
Pittsburgh, United States, 34 minutes ago
United Kingdom, 39 minutes ago
United Kingdom, 52 minutes ago
France, 3 hours ago
United States, 30 minutes ago
Pittsburgh, United States, 34 minutes ago
United Kingdom, 39 minutes ago
United Kingdom, 52 minutes ago
France, 3 hours ago
Traffic: 780 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