checking a list of packages that I just updated, I find some
that don't have info on patch level changes, some that have a news
file but whose must current entry is for an old release, and one that
DOes have patch level NEWS...bioc-devel at r-project.org
>>> Subject: Re: [Bioc-devel] knowing what is changed/new in release
patches
>>>
>>&…
Order by: Relevance
dear All,
was there any change to the biomart web service recently? Today I stumbled over the following problem when I wanted to list all available...line 4 and html
6: Premature end of data in tag html line 2
></pre>
I guess something had changed at the biomart web service.
cheers, jo
My R/Bioconductor:
<pre>
> sessionInfo()
R versio…
abs(log2FoldChange) > lfc.cutoff_0.5)
>up_padj_
```
But I have exactly same results if I change the order and use "dpi14tocv" as baseline
Can someone help me to understand why??
Thanks
we're currently using. On the other hand, our
method works well in our hands! So you see my dilemma... changing
something that works in order to make some savings...
Any comments appreciated!
Jose
--
Dr. Jose I. de las Heras Email: J.delasHeras
updated 18.5 years ago • J.delasHeras@ed.ac.uk
genes but instead they are reported to be significantly differentially expressed with huge fold changes.
Has someone experienced this before or have any advice on how do account for such genes with large variation in counts
updated 22 months ago • Sneha
to produce pie charts or similar with percentage of genes
associated to selected Gene Ontologies categories (or KEGG),
preferable if I can choose the categories so that I can customise them
using some search by keyword option...like to do it to compare the percentage of genes expressed in
two different samples for the selected categories.
I have explored Voronto (outside Bioc) and goProfiles and …
updated 12.9 years ago • Jose M Garcia Manteiga
<div class="preformatted">Hi all,
It looks as if the as.vector call to a run length encoded factor turns
it to a vector of characters.
Did this happen on accident, or was it a deliberate design decision?
Previously:
R-2.12, IRanges_1.7.19, GenomicRanges_1.1.20
(A factor of length one is returned):
R> a <- Rle(strand(c('+', '-', '+', '+', '-')))
R> as.vector(a[1])
[…
gt; > Many thanks for your quick and very comprehensive response.
> >
> > From your comments, I have one more question related:
> >
> > (1) I understand your comments about the intron control
transcripts,
>...gt; but I do not fully understand the rescue transcript category that
I
> > have also obtained in my topT…
updated 12.1 years ago • María Maqueda González
that GOstats hyperGTest comes out with.
Am I right in thinking the p-value is for enrichment of each category
individually (i.e. NOT corrected for multiple testing)?
I'm analyzing array CGH data so I am testing a lot of categories...my
universe is all human genes that have a chromosome position, GO
category and entrez ID). Below is an example result - my
interpretation is that I shouldn't get s…
updated 18.0 years ago • Janet Young
deployLocation=*illuminahiseq_rnaseqv2*][name=*Level_3*]'</pre>
1. Is this because of the recent changes in TCGA? TCGA has posted the following info on their website " 06/10/2016 - __Announcement :- ____As the
updated 9.5 years ago • sabarinath.chandrasekharan
all,
I am a PhD candidate in Beijing Institute of Genomics,
Chinese
Academy of Sciences. Recently I have been worked with data analysis
concerning RNA capture followed by high throughput sequencing. Four
samples...for my project, I could just calculate RPKM value for
each
gene, and identify DEGs simply by fold change > 2? Thank you!
Sincerely,
…
updated 12.3 years ago • 邵建明
I found all the data are negative, the downstream function only works on positive value.
How can I change the parameter of `vsn` , them the output can be positive value?
Thank you in advance for great help!
Best,
Yue
<img alt="Screenshot
updated 5.0 years ago • yueli7
scater package, that I am using for single-cell RNAseq analysis of 10X data. I wish to change the size of the points and also remove the gray outlines that currently appear around the points.
I tried using "scale
updated 7.7 years ago • CodeAway
at="gmail.com=">
> To: bioconductor at r-project.org
> Subject: \[BioC\] edgeR: fold change reported by exactTest for zero values of rna-seq
>
> I have used the exact test in edgeR to compute the log fold changes...expression in all samples
> belonging to one of the two conditions. This would make the fold change
> mathematically …
updated 11.0 years ago • Gordon Smyth
black
agouti3 129 black
agouti5 129 black
I want to test which genes change their expression when the
environment changes, controlling for the genetic background. I am
using DESeq2 for this...environment.
However, the choice of the base level for the factors in my
experimental design changes the genes that are significant. If I leave
the default reference levels (129 for g…
3 replicates for each sample, choosing DESeq2 as the analysis method), peaks with very small Fold-change were found to be statistically significant.
I have plotted an MA plot; the red points are the significant ones, the black...I'd like to ask whether you agree that it's surprising/strange that lots of peaks with a very small change became significant. There are no non-significant peaks above…
Best wishes
Gordon
On Thu, April 27, 2006 2:00 am, Jenny Drnevich wrote:
> Hi everyone,
>
> Comments from Naomi and Gordon (below) about the technical
replication in
> the 2x2 factorial loop experiment are very close...replicates, which leads to artificially lower p-values.
This
> combined with even minor changes to the variance components can lead
to
> …
updated 19.7 years ago • Gordon Smyth
Hi there!
I have a differential expression data set, consisting of a list of gene handles, their log2-fold expression change between two conditions, a p-value for that change, and annotated GO terms. It looks basically like this: https://www.dropbox.com/s/bswzujqx07t4lr2/VirtualBox_ubuntubox_11_11_2020_12_44_16.png?dl=0
I am currently working in R, and would like to do a GO term enrichm…
updated 5.1 years ago • lessismore
I look at the statues and see that most genes are category 4
```r
> table(normalisedData[["convergence"]])
0 1 2 3 4
3049 516 4615 1 8098
```
Category 4 is "baseline selection didn't coverge
updated 4.7 years ago • Dario Strbenac
Hello,
Is there a way to test for differential binding above a log2 fold change threshold in the dba.analyze() portion of DiffBind? I understand we could use the fold argument in dba.report() to extract...in one group over the other. According to Section 2.12 ("Differential expression above a fold-change threshold") of the edgeR user's guide, such hypotheses should undergo thresholded t…
updated 9.6 years ago • le2336
Hello Bioconductor community,
I have used DESeq2 to test for differences in the overall transcriptional activity of species in a microbiome sample. However, i am not quite sure whether what I'm doing is correct. Thus, I would be very thankful for somebody confirming that this solution makes sense or pointing me to an error.
I am comparing two different biological conditions. For each condition,…
updated 4.7 years ago • Tom
<div class="preformatted">Dear list,
I am getting an error when trying to parse the latest msigdb version
from Broad. I suspect the problem is due to that Broad added another
category (c6). Will the new category be included in GSEABase? Is there
a way to parse only categories c1-c5, or an alternative way to get all
categories?
See the R code and versions below.
Thank you!
Best regards,
…
updated 12.9 years ago • Lina Hultin-Rosenberg
that
allows me to use use HyperGTest with custom lists.
All I have to turn the list of categories in to a binary matrix, where
my
rows are my genes, and the columns are the different categories and
the
entries in...gt; > pathways, but unfortunately none showing me how define my own very
> > limited set of categories.
> > You are exactly right, in that I want to …
the dosage and working mechanism of soma visit here at Health Naturo: [https://healthnaturo.com/category/soma-pills/][1]
[1]: https://healthnaturo.com/category/soma-pills
updated 2.2 years ago • healthnaturo1
for the
5 odd columns of interest, and NULL for the 77 odd unwanted columns in
a gpr file
The change is to the following code in read.marrayRaw:
comment out;
# h <- strsplit(readLines(f, n = skip + 1), split = sep)
# h <- as.list(unlist
updated 22.5 years ago • Marcus Davy
I have used the exact test in edgeR to compute the log fold changes. Here is the snippet:
<pre>
d <- DGEList(counts=counts, group=samples$Condition)
d <- calcNormFactors(d)
d <- estimateCommonDisp...in all samples belonging to one of the two conditions. This would make the fold change mathematically undefined (di…
updated 11.0 years ago • Nick N
group B, hence contrast B versus A logFC =4 with adjusted-P = 10^-20). I am concerned that such fold-changes may be exaggerated. I am aware that voom calculates CPM using a prior.count of only 0.5, whereas the cpm() function uses
updated 3.0 years ago • vm
<div class="preformatted">Dear Lukas and Bioconductors,
I have been asked to look at a MeDIP-Seq dataset that has been
processed
with a previous version of the MEDIPS package (version 1.2.0) and I've
noticed there have been some changes with regards to the current
version
I have installed (version 1.10.0). In particular, it appears as
though
the whole concept of AMS (absolute methylation …
updated 12.4 years ago • Jonathan Ellis
seems* to work under 1.8.0, but you are welcome to report odd
things you would notice). We made some recent
changes in our code to try to speed it up (because it was
slooooow, and still is), which hopefully did not introduce
bugs
<div class="preformatted">Hello BioCer's,
I've been using affycoretools, particularly limma2annaffy,for a while
now and love it. These wrappers really make life simpler.
However (there was bound to be a however), in a recent experiment I've
had some problems with vennSelect. The experiment has 4 groups and 4
time points, 5 replicates each. There...love it. These wrappers really make l…
Hi,
I have a list of differentially bound sites between conditions and would like to export lists defined by 2 things: fold change between some positive or negative value given the condition and specific FDR cutoffs. If anyone has advice on how to...bound sites between conditions and would like to export lists defined by 2 things: fold change between some positive or negative value given the con…
updated 8.9 years ago • rbronste
gr <- GRanges(seqnames = c("1", "2"), IRanges(start=c(1000, 2000), width=100), strand = c("+", "+"), category = c("A", "B"))
I would like to split `` gr `` based on `` category ``, in order to have a `` GRangesList `` that would be similar to:
grl <- GRangesList
updated 7.1 years ago • unamourdeswann
<div class="preformatted">Hi.
Below is an outline of the code I am using to analyse two colour array
data.
Normal = Cy3
Case = Cy5
There are 3 replicates.
Can the fold change be reported back in the siggenes.table? From the
documentation, it is not obvious how this is done.
Thank you for any help...to analyse two colour array
data.
Normal = Cy3
Case = Cy5
There are 3 replicates.
Can the …
odd when plotting tracks on a pdf device (postscript turns out fine),
this only happens to some recent R-devel versions (tested on three
r-devel builds Feb.3, Feb.14 and Feb.18), apparently the build machine
in Seattle is...not yet affected, which has a devel build on Jan.15.
This
happens to the most recent devel version of Gviz 1.7.7.
Here is an example, can't really figure it why,
############…
have checked both the box and MA plots using both raw and normalized counts and there is very little change.
I am looking at H3K27me3 ChIP-seq data between two different tumor subtypes (i.e BRAF vs RAS). When using edgeR many...lt;- dba.count(dba, fragmentSize = 1000, minOverlap = 2)
dba.contrast <- dba.contrast(dba.count, categories = DBA\_TISSUE)
\#DESEQ2
dba.analyze &l…
updated 9.1 years ago • cnova1950
just greyed out.
Data is a csv file with two columns: gene name in KEGG format, then log2fold change values in the second column.
Code is below.![enter image description here][1]
```r
> data <- read.csv("pathview_input_AN_OX.csv...header=FALSE)
> geneList = data[,2] #importing fold change data as a vector
> names(geneList) = as.character(data[,1]) #addin…
updated 10 months ago • Jessica
I'm trying to run a straightforward Wald test in `` DESeq2 `` and was a little surprised to see that fold changes and standard errors are no longer shrunken by default. I know I can still compute moderated values using the `` lfcShrink() `` function, but I see no straightforward way to:
a) calculate the corresponding test statistics and _p_-values; or
b) implement the gene filtering, LFC thresh…
updated 8.1 years ago • david.watson
enrichment for my data which
is not built-in oraganism.
>enriched.GO=unsorted_L14.15_S_GO.wall$category[p.adjust(unsorted_L14.
15_S_GO.wall$over_ represented_pvalue, method="BH") < 0.05]
> head(enriched.GO)
character...BP",
"GO:MF"), method="Wallenius", repcnt=2000, use_genes_without_cat=TRUE)
Using manually entered categories.
Calculating the p-values...
> head(unsor…
Hi,
I am trying to address the question which genes associate with change of the metabolite levels following the diet. I have paired samples (before and after the diet). I have previously asked...factors (at least a RIN)
```
design <- model.matrix( ~ ID + RIN + Timepoint)
```
2) Gordon commented previously
```
"Even if you included Metabolite in a completely different non-paired …
updated 5.2 years ago • anna.cot.anna.cot
arrange(desc(logFC))
```
```{r}
library(msigdbr)
hs_immune_df <- msigdbr(species = "Homo sapiens",
category = "C7",
subcategory = "IMMUNESIGDB")
```
```{r}
ranks <- deframe(res2)
head(ranks, 20)
```
```{r}
fgsea_SHH <- fgsea(pathways = hs_immune_df, stats...r}
library(clusterProfiler)
```
```{r}
hs_immune_df <- …
updated 2.6 years ago • pg45863
TopologyGSA, DEGraph, clipper, SPIA, TAPPA, PRS, PWEA with a custom list of fold-changes and associated p-values rather than having these functions run a DE analysis internally?
It doesn't seem so from the
updated 9.0 years ago • rubi
of
bioconductor developers, if there is a function to
generate a heatmap of all enriched GO categories after
a conditional hyperGTest.
For example, I have 5 different time points
time-series data and with 3 different...doses. I run
HyperGTest and I endup with atleast 50 categories for
5 time points and 3 drug treatments.
3hr @ d1; 3hr @ D2 ; 3 hr @ D3 - 50, 50 ,50 cats
respectively.
Like wise …
updated 18.0 years ago • Srinivas Iyyer
for differential expression and found that DESeq2 mysteriously inverted the sign of a subset of fold changes. According to [this discussion][1], turning off fold change shrinkage should make log2foldchange from DESeq2 be simply...counts group B) / (mean of normalized counts group A).
However, it seems that some degree of fold change moderation is done even when betaPrior is False.
As an example…
updated 5.0 years ago • Yanling
when I try
to re-run old scripts. I've never had this issue
before, but updated from 2.6.1 to 2.7.0 recently.
Any help/comments would be much appreciated! The full
list of commands + sessionInfo is shown below. I've
tried with
Phred+64,FastqQuality=Phred+33) is",score_sys,"\n")
it is a Phred+64 system, how can i change the qual to Phred+33. then i
can
make new reads by
reads <- ShortReadQ(sread=seqs, quality=qual, id=
BStringSet(paste0(sample
updated 11.6 years ago • wang peter
<div class="preformatted"> Hello Bioconductor Users,
Sorry to bother you, but I have a couple of quick questions on the
affy package that I have been unable to answer by reading through the
textual description of affy available on the bioconductor website and
the recent papers on the subject. Iin general, am very impressed with
the noise reduction using affy and truly appreciate the Bioco…
updated 22.8 years ago • Luckey, John
<div class="preformatted">Hello Bioconductor Users,
Sorry to bother you, but I have a couple of quick questions on the
affy package that I have been unable to answer by reading through the
textual description of affy available on the bioconductor website and
the recent papers on the subject. Iin general, am very impressed with
the noise reduction using affy and truly appreciate the Biocond…
updated 22.8 years ago • Luckey, John
<div class="preformatted">On Wed, Oct 02, 2002 at 02:09:00PM +0200, Jesper Ryge wrote:
> Hi laurent
>
> I am using the affy package for R. I just have one question. I
tried to
> read a cell file and plot it with image(cel.file). That works fine,
except
> the image is turned upside down! It is a rat neuro chip, so there
is a
> control sequence i…
Hi all,
Can anyone point me into the direction on how to achieve the subject
line?
I'm using right now the "CustomEndNodeList" from "goTools", retrieve
two
consecutive ranks and accept only what I retrieve with the higher rank
and
not with the lower ... but GO has rank-skipping connections and I
would
prefer to really be able to slice the tree at level x below ID y while
disregarding those ...
…
Hi Josh,
I was wondering whether you got any response to this problem. It is
quite
old, but I just encountered the same problem.
If so, I would appreciate it, if you can help
Thanks,
Assa
[[alternative HTML version deleted]]
updated 14.8 years ago • Assa Yeroslaviz
Hi Josh,
I was wondering whether you got any response to this problem. It is
quite old, but I just encountered the same problem.
If so, I would appreciate it, if you can help
Thanks,
Assa
Assa Yeroslaviz
Application service, Bioinformatics group
Max Planck Institute for the Biology of Aging
Robert-Koch-Str. 21
50931 Cologne
Germany
phone: +49 221 47889793
e-mail: AYeroslaviz at age.mpg.de
updated 14.8 years ago • AYeroslaviz
appreciate your advice on the results(contrast) section of my analysis.
I have 5 disease categories(RM, RP, SP\_progress, SP\_stable and healthy) for each category we extracted monocytes and treated these monocytes...within each group by comparing monocytes with different treatment compositions (Eg: For disease category RM, I am interested in comparing 10nm vs 100nm, 10nm vs 50nm, 100n…
Hi,
I am running into truncated phenotype categories when I use GRASP2 like this:
<pre>
> library(grasp2db)
> GRASP2() %>% tbl(., 'study') %>% filter(PaperPhenotypeDescription...in cystic fibrosis
</pre>
</td>
</tr>
<tr>
<td>
<p> </p>
<p>Although cystic fibrosis-related categories in GRASP web page are…
updated 10.1 years ago • gokcen.eraslan
How to extract top DEG using limma at threshold value p<0.05 and fold change >1.5 ?
I request you all too kindly suggest the R script for topTable.
topTable(fit2, coef=2, ……?????????)
Thanking you.
 
updated 8.6 years ago • rkp
Hello,
In a previous version, I was able to read a tabix file, including the
first line that started with # and had column names. Now with
Rsamtools 1.8.4, it skips that line and the first element of the
character vector is the first record of the tabix file. Any way to get
the old behaviour back so that I can know the column names ?
anno <- "http://genomesavant.com/savant/data/hg18/hg18.ref…
updated 13.6 years ago • Dario Strbenac
nbsp;
I have just read the vignette about DESeq2 and I have a question about shrunken log fold changes and threshold test.
I use DESeq() and results() functions to get the gene set with absolute LFC > 1. I understood that the
updated 7.1 years ago • corentinrichard374369
as hours-minutes-seconds or universal time with proxitct. Both occasions cause the output of time to change to a numerical value that is not understandable in the context of time.
Example:
mod = model.matrix( ̴ factor(Case_Control
an iteration that works. However, when I modify the gRNA.size to be 24, I get a weight error. When I change the weight commant to rep(1,24), the error changes to a column error. I am stuck.
```
library(CRISPRseek)
library(BSgenome.Mmusculus.UCSC.mm10
updated 5 months ago • Citrus
I have a problem working with GO annotations.
I would like to group my data according to their GO categories, but
only of
one level.
I have a data.frame (three columns: WT, mutation, mean(WT/mutation)
and ca.
3150 rows)
row.names...0.04276977 40.295400
2361_Trmt5 1.0203870 0.03652034 27.940238
I also have the GO categories for each of this rows( the names are MGI
symbols from the mou…
updated 14.8 years ago • Assa Yeroslaviz
<div class="preformatted">Hi,
I know that I should sent to the list rather than you. That's why I
sent a followup message to the list.
By default, I click "reply" rather than "reply to all". I would
suggest that the "reply-to" field in any message in the mailing list
be changed to the mailing list address. This would avoid some messages
not being forwarded to the mailing list.
Regards,
P…
updated 4.9 years ago • Peng Yu
Recent ...
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