div class="preformatted">Hello,
Can anybody advise me on how to get gene-level rma vs. probe-level rma
using rma(...) method in the Affy package for the HTHGU133A platform?
Thank You,
Aaron
[[alternative HTML
Order by: Relevance
give an input csv file containing genes
relevant.genes <- factor(as.integer(all.genes %in% data)
names(relevant.genes) <- all.genes
GOdata.BP <- new("topGOdata", ontology='BP', allGenes =
relevant.genes, annotationFun = annFUN.db...affyLib = 'hgu133plus2.db')
------------
Error in .local(.Object, ...) : allGenes must be a factor with 2
levels
> str(relevant.genes)
F…
DMRcate package). However, I keep getting this error:
Error in .local(GdObject, ...) :
'groups' must be a vector of similar length as the number of rows in the data matrix (19)
```
GRset <- preprocessFunnorm(methylset)
betavals...lt;- data.matrix(betavals)
disease <- c(UlcerativeColitis="magenta", Normal="forestgreen")
names(disease) <- levels(factor(met_annot$Chara…
updated 5.1 years ago • Julie
<div class="preformatted">Hi Karl, Seth,
This problem is probably caused by the SJava version you are using.
There
has been an update recently of SJava to SJava 0.68. Appearantly some
functions of SJava return a different data type, which causes errors
in
RMAGEML. I only spotted this very recently and haven't had time to
update
RMAGEML. I'll do this as soon as possible. For now, you sho…
subset of this eSet a new eSet is created. However, the factor variable retains all of its original levels , even when they do not exist in the new eSet , how I could drop this levels?
table(pData(eset)\[ ,"Disease"\])
these are the levels...cancer
but after subseting my eSet dosn't have sample's related to node negative but their level are exist in the data
updated 9.7 years ago • Shamim Sarhadi
DE
analysis.
The only thing that while I don't find it surprising but still puzzles
me, is the high level of the errors. The confusion matrix gives me a
level of misclassification error of 0.1 and 0.6 for the two classes,
and...an overall error of 0.3
Please, can somebody help me comment on this? Do the error levels of
the PAM analysis invalidate in some way the results obtained with the
two DE …
div class="preformatted">Dear All
I have just seen a result which makes me either suspect the validity
of
print-tip loess normalisation, or wonder if there is a bug in
bioconductor.
I am performing print-tip loess normalisation
updated 21.5 years ago • michael watson IAH-C
GOseq on a list of diffentially expressed genes and I would
like to do an analysis at a specific GO level (level 4 for example)
instead of the complete GO.
Is there a tool in GOseq that already does it ? Or do I have to
prepare the file
chr10")
__\#\# Error in .normalize\_seqnames\_replacement\_value(value, x) :
\#\# levels of supplied 'seqnames' must be identical to 'seqlevels(x)'__
GenomicRanges:::.normalize\_seqnames\_replacement\_value...nbsp; runValue(value) <- factor(runValue(value))
\#\# if (!identical(levels(value), seqlevels(x)))
\#\#&n…
updated 9.1 years ago • wcstcyx
How to extract gene level methylation values?
I used Bismark to align BS-Seq data followed by methylKit for differential methylation identification...the analysis considers CpG sites, but by using suitable annotation BED file, we can perform region level (promoters, exons, TSS) analysis. I was wondering how to obtain gene level methylation values
updated 4.4 years ago • ag1805x
Dear Bioconductor community,
based on a current project aiming to decipher prognostic biomarkers that driving the response to chemotherapy in breast cancer, we are trying to analyze external public datasets to validate in house findings; on this premise, on an rnaseq gene expression dataset of neo-adjuvant treated patients with multiple time points:
T1 is the “pre-treatment” timepoint, T2 …
updated 4.4 years ago • svlachavas
following error:
```r
Warning messages:
1: Computation failed in stat_signif():
'x' and 'g' must have the same length
2: Computation failed in stat_signif():
'x' and 'g' must have the same length
```
We would greatly appreciate
updated 2.8 years ago • Elif
<div class="preformatted">Hi I am a novice in both R and EdgeR. I have a readcounts tab
seperated file (with around 24 conditions belonging to 6 different
groups with its first column containing the tag identifiers and the
other columns containing the read counts. I used read.delim function
in R in the following manner :-
seq_data <- read.table("newfile.txt", header = TRUE, sep = "…
fitting on my data but i keep getting the
following error
Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric
But I'm not sure what the problem is does anyone have suggestions?
Here's what i've been doing after normalization...data, dim 39693 240
fit <- lmFit(expr,design)
Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric
Thanks,
.kripa
[[alternative HTML version …
nbsp;
Invalid keytype: Ensemble. Please use the keytypes method to see a listing of valid arguments.
My probes look like this:
\[997\] "TC0100013150.hg.1" "TC0100013155.hg.1" "TC0100013156.hg.1" "TC0100013158.hg.1
updated 6.9 years ago • Pindre
Error in .normargSeqlevels(seqnames) :
supplied 'seqlevels' cannot contain duplicated sequence names</pre>
---
It's quite clear that there must be some duplicates either in the bam file or in the exonsBy object. However any combination...of duplicates(ebg), which(duplicates(names(ebg)), etc. that I could try returned no duplicate.
=> __hence my question__ : how to narrow down t…
updated 7.8 years ago • c.legrand
your questions:
#1: The UPC probability represents the "probability the gene is
expressed at a level above the background." So it really depends on
how confident you want to be. If being 50% confident that the gene is
active...Cc: "SCAN.UPC Maintainer" <stephen.piccolo@hsc.utah.edu>
> Subject: [BioC] SCAN UPC probability - validation of gene expression
> results using U…
normalization i could get the same gene list, but all GOs will have approximately similar level of depth on GO tree (the same level of specificity). I think that with GOSim or GOSemSIm bioconductor packages possible
Basically GCRMA changed it's BG parameter estimation from using a low
quantile of strata of affinity levels (1.1.0 or less) to a smoother
way
using loess. There is also a fast=FALSE option which does not use the
(default) faster ad...default(fast=T) version is used. To me this questions whether the
statistical test would still be valid, also it raises questions about
estimating true/false -/+tive…
Suppose I have run deseq like this:
```
my_coldata$varA = factor(mycoldata$varA, levels=c('control', 'case')
my_coldata$varB = factor(mycoldata$varB, levels=c(0,1))
dds = DESeqDataSetFromMatrix(
countData=my_counts...I can access the metadata with `colData(deseq_obj)` but it comes as a matrix with factor and level information wiped out. Is there a way to access this information?
…
mixes with statistics. I come from the
Machine Learning field, and usually have problems with the naming
conventions (well, among several other things, I must admit). Besides,
I am not an expert in statistics, having used the barely...necessary for
the validation of my work.
Well, let's try to be more precise. One of the topics I am working
more right now is the analysis of methylation...Is ther…
workflow of microarray analysis such as background correction, normalization. However, I have a gene-level expression data matrix was obtained using `RMA`, and I intend to run `PCA` for the purpose of dimension reduction for the...features.
Essentially, I have gene-level expression data matrix (32830 features of rows, 735 genes of columns), and I have profile data of the target (735 rows and.…
updated 6.5 years ago • Jurat Shahidin
by @bioc-issue-bot, bump the version and recommitted (webhook set). I got a message saying it was a valid push, however, there is no new report since yesterday. Would anyone know how long should it take to get a response? Thank
updated 5.7 years ago • whou10
normalized values.
My concern is that running RMA normalization on only 3 replicates is
not a
valid use of the method. Can anyone offer advice on the number of
replicates necessary to run RMA normalization, or if other
updated 15.7 years ago • Kaitlin Louise Bergfield
working on a project that has exactly the same design
as the example given in Section 9.7 multi-level experiments of Limma
package's user guide. But our questions about the contrasts are
slightly different: 1) what's the...Diseased.B-Normal.B)/2,
+ TissueBvsTissueA = (Normal.B-Normal.A +
Diseased.B-Diseased.A)/2,
+ levels = design);
Am I right?
Tremendous thanks for your help.
Y…
pathways for
Drosophila and not C Elegans. For C Elegans you should use the sce
instead of dme. The names of CH and the vector CH1 must be valid
ENTREZ IDs for the respective organism.
Adi Tarca
[[alternative HTML version deleted
ath1121501.db").
genenames <- org.At.tairGENENAME[ids] #map the probe ids to the
gene names in TAIR
The output of which is AnnDbBiMap[1]
number<-org.At.tairENTREZID[ids] #map the probe ids to the gene
ids in TAIR...in this step and unable to proceed further.The error
reads:
Error in fix.by(by.y.y): 'by' must specify uniquely valid
column(s)
Is it because…
updated 13.1 years ago • Guest User
D human Gene chip assays. I understand that there are two ways of look at the data: from a gene level and from a probe set level.
Using the *RMA* algorithm, I can summarize the exon data on a **gene level:**
```r
probeset.eset=rma(dat...target="core")
```
or on an **probe set level**
```r
probeset.eset=rma(dat, target="probeset")
```
But how do I get the expression data on a **transcri…
updated 5.0 years ago • mailtoshivam13
Hello,
I've carried out a number of differential expression analyses using the Limma-Voom pipeline for a rather complicated data set. I'd just like to clarify that my approach detailed below is appropriate.
The design of the experiment is very much like those described in sections 9.6 and 9.7 of the Limma manual (time-course experiments and multi-level experiments).
Our data set compris…
factor`(`*tmp*`, ri, value = "normalizeCtData(q = sr.norm,
norm = \"quantile\")") :
invalid factor level, NAs generated
2: In `[<-.factor`(`*tmp*`, ri, value = "normalizeCtData(q = sr.norm,
norm = \"quantile\")") :
invalid factor level, NAs generated...q.norm, remove.category="Undetermined",
n.category = 36, remove.name=c(HK.miR.rm,"MammU6"))
Error in names(x) <- value :
'name…
<div class="preformatted">Dear Bioconductor users,
I am working with differential expression at the transcript (isoform)
level. I have 6 different conditions (2 replicates/condition).
I want to know if I can use DESeq2 for that or if the package can only
be
used at the gene level.
Thanks,
Alicia
--
Alicia R. Pérez-Porro
PhD candidate
Giribet lab
Department of Organismic and Evolutiona…
have a question regarding underlying theory for significant probes and genes identified by a.) probe level differential methylation analysis using limma and b.) region level differential methylation analysis with regions...Why is there only around 12 percent overlap between significant CpGs identified at probe and region level**
2. (Likely will be answered by Q1) **Why are there only 31 signific…
updated 7 months ago • jamiecatalano2
have access to 8 samples (each corresponding to one colon section). My question is, if it is still valid to use SingleR in that case, or if the sample size of the reference is too small. I noticed that in the [vignette](https://bioconductor.org
updated 16 months ago • nhaus
Hello,
I run DESeq2 with multilevel. For each of the levels, I run "results" with the desired contrast between pairs of conditions. When I run resultsNames, I noticed that output...refers to the first level as background. Also, lfcShrink shows different condition for "_log2 fold change (MAP)_" and "_Wald test p-value_". Here...but I am willing to share more offline.
<pre&…
a sample
belongs to.
2) Determine how stable these prediction sets are through some sort of
cross-validation (I would prefer not to divide my set into a training
and test set for stage one)
These steps fall into the supervised
updated 15.9 years ago • Daniel Brewer
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
```
It will be great to get...DESeq2.
I run the DESeq2 in my old machine and it runs without issues which means that the column names in the counts are same as the row names of the coldata…
updated 3.0 years ago • Cherif
Hi all,
I've HuEx ST1.0 microarray data. Using Oligo package I get gene level expression (RMA, target=core) and for exon probes I get expression using RMA (target = probeset).
I'd like to map the...probesets from exon level expression to genes.
I've HuEx-1\_0-st-v2.na36.hg19.transcript.csv and HuEx-1\_0-st-v2.na30.hg19.probes…
updated 7.1 years ago • GENOMIC_region
<div class="preformatted">Hi BioC,
I have question about LIMMA makeContrasts( ) function. I am reading
parameter
file for LIMMA from out side R environment and building design matrix.
G1 G2 and G3 are Group names coming from parameter file.
> Groups <- c("G1","G2","G3");
> colnames(design) <- c(Groups);
> design
G1 G2 G3
1 1 0 0
2 0 1 0
3 0 1 …
In others words the purpose of my analysis is to obtain for each gene a ranking list of expression level in tissues, that I could sort it in decreasing way in according to expression level or I could show the results for each...function and the difference among following example:
1) makeContrasts(B-A,C-B,C-A,levels=c("A","B","C"))
2) makeContrasts(contrasts="A-(B+C)/2",levels=c("A","B…
updated 10.3 years ago • elisa.micarelli
score only i'am getting an interaction. So, i want to ask **whether this low confidence score is valid for this short gene set related to Homo sapiens** or else what should i do in this case
Hello!
We have data from a bulk RNASeq study at a transcript level (young adults mice's hippocampus data), and we want to know if there is any known scRNASeq reference study in mouse's brain...at a transcript level to do a cell type deconvolution analysis.
Does anyone have any experience with that?
Many thanks!
Marc
a CNA object from a oligoSnpSet matrix after applying the crlmm package
I keep getting "genomdat must be numeric" error from my
oligoset<- OligoSetList(cnSet3, batch.name=batch(cnSet3)\[1\])
oligo<-oligoset\[\[1\]\]
CNA.object
updated 10.4 years ago • perdomos
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 9.5 years ago • Thomas Sandmann
but with no success.
- Second, after data import I would like to retrieve all
information on a probe level for several probe sets. I do
this using the pm()-function, for instance
>pm(CelFiles)[1:16, 1:50]. The problem is that I have to...in advance,
Roel Verhaak
-------------- next part --------------
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File","Factor Value[compound]","Factor Value[dose]")]
Treatment <- SDRF[,"Factor Value[dose]"]
levels <- c("NA","1","4")
Treatment <- factor(Treatment, levels=levels)
x <- read.maimages(SDRF[,"Array Data File"],
source="agilent", green.only...201:205,]
Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are …
updated 2.8 years ago • Joshua
div class="preformatted">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...to perform
an initial filtering on either Present Marginal or Absent calls, or on
gene-expression levels (so that only genes with an expression > 40,
say, after scaling to a …
Hi,
When I checked articles to find a method to identify predictors of overall survival, mostly glmnet cox model is used with Lasso penalty and cross validation. As cross validation, people used 10-fold cross validation with 1000 iterations or LOOCV.
I read about glmnet method and searched forums for codes. I found two different approaches for 10-fold cross validation: first one is running fi…
updated 6.3 years ago • Talip Zengin
me the error :
"Error in spia(de = DE_top, all = ALL_top, organism = "hsa", nB =
2000, :
de must be a vector of log2 fold changes. The names of de should
be included in the refference array!"
Would you know what the problem...is? The fold change column from the
contrast.fit method was not given as logFC, so I changed the names of
the columns to FC. Would that be the issue?
I have attached …
Hi,
I'm wondering if it is valid to do comparisons, such as a t-test for a gene between different treatment groups, on VST or rlog transformed data. While
classify the samples. As I do not have a
test
and training set I am using Leave-one-out cross-validation to help
determine the robustness. I have read that one should perform gene
selection for each split of the samples
following experiments:
T_1_vs_Vehicle_1
T_2_vs_Vehicle_2
The following valid label columns were detected:
126, 127L, 127H, 128L, 128H, 129L, 129H, 130L, 130H, 131L.
Error in importCheckExperimentNames...expNames = expNames, dataframes = data) :
The names of the data objects in 'data' differ from the names given
in the Experiment column…
updated 6.9 years ago • kkim369
in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
In range 21: 'end' must be >= 'start' - 1
updated 3.2 years ago • User000
lt;- TxDb.Hsapiens.UCSC.hg19.**knownGene
>
> Specifying use.names = TRUE puts the transcript names on the
GRangesList.
>
> introns <- intronsByTranscript(txdb, use.names=TRUE)
>
> Unlist and remove duplicate introns...The select() function can map txid to geneid (and others). See
?select.
>
> txnames <- names(intronsNoD…
updated 12.8 years ago • Fong Chun Chan
Error in buildXYData(table, status, main, display.columns, anno, counts, :
Length of groups must be equal to the number of columns in counts.
The R feedback was
4. stop("Length of groups must be equal to the number of columns
Hello,
I am running DESeq2 with this metadata table -
| Condition | Time | Batch |
|-----------|------|-------|
| Control | 0h | 1 |
| Control | 12h | 1 |
| Control | 24h | 1 |
| Control | 0h | 2 |
| Control | 12h | 2 |
| Control | 24h | 2 |
| Control | 0h | 3 |
| Control | 12h | 3 |
| Control | 24h | 3 |
| Control | 0h | 4 …
updated 12 months ago • bhandary.8590
div class="preformatted">Dear Group,
table(Rle) seems to ignore empty levels.
x = Rle(c(2,3,1,2,3,2),rep(2,6))
levels(x) = as.character(0:5)
table(x)
table(factor(as.numeric(x),levels=as.character(0:5)))
I am using R 2.15.1
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070705/
c56a6069/attachment.pl</div
updated 18.4 years ago • carol white
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080329/
4ef93d4b/attachment.pl</div
updated 17.7 years ago • Kathy Duncan
class="preformatted">Hi Group,
Is there any function which would help in converting data from probe
level
to gene level by averaging the expression of all the probes
corresponding to
a gene.
For eg:
array1 array2
probe 1 Gene
updated 14.9 years ago • viritha kaza
I please ask a question
I get very different results when I perform Deseq2 by choosing 3 factor levels under 1 FACTOR vs performing Deseq2 individually 3 times to compare the three factor levels to each other So, I am unable...Factorlevel 2:conditionB
Factorlevel 3: conditionC
(I also checked the box that says :Output all levels vs all levels of primary factor (use when you have >2 le…
updated 4.3 years ago • gayathrig
Recent ...
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ATpoint
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Answered here: https://support.bioconductor.org/p/16318/
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