Bioconductor Forum

successful in remediating the issue to get all packages downloaded to my library path.  > source("http://bioconductor.org/biocLite.R") Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help A new version...also installing the dependency ‘genefilter’   There are binary versions available but the source versions are later:     &am…

r

updated 8.8 years ago • Alexistbrown17

mechanism. As for modifying the code for your project, you will want to download and unpack the source packages (.tar.gz) for Category and GOstats. The code is split between these packages since much of the Hypergeometric...is not GO specific. There are a few notes in the man page for hyperGTest for how to extend to other category types if that is what you want to do. Given that you didn't hav…

GO Cancer GOstats Category GO Cancer GOstats Category

updated 18.7 years ago • Seth Falcon

<div class="preformatted">On 10 Jun 2010, at 17:54, Ina Hoeschele wrote: > Hi, I have been analyzing an affy microarray dataset with 2 treatments and 1 control, which do not have replication (so total of 3 chips), with several methods that do not require replication, including bgx. BGX seems to give the poorest results which I did not expect, so I am wondering whether I am doing som…

Microarray affy bgx Microarray affy bgx

updated 15.6 years ago • Ernest Turro

Hello all, I have a question regarding the cnetplot from the clusterprofiler package in R. As shown in the first figure, the number of nodes appear in my cnetplot is too many that many data points (genes) are unlabeled. It seems that all genes in my gene list that belong to a certain category appear in the plot regardless of their FC values. Is there any way that I can reduce the number…

cnetplot R clusterProfiler

updated 2.9 years ago • YNKIM

gene, gene A and I have do DESeq2 analysis between cancer and normal. The result is, gene A logFold change is 2.5, which is upregulated in cancer with p-value 0.01. The baseMean is around 35. What I want to do is to generate a dummy...data for each category, cancer and normal which will have baseMean 35 and if it is caluclated back, it will give 2.5 log fold change with 0.01...negative binomial …

deseq2

updated 9.8 years ago • bharata1803

I have received my RNAseq data recently as EXCEL and txt files.I think that they are already normalized. When I open txt file in R studio, I can have RPKM, P value...I have received my RNAseq data recently as EXCEL and txt files.I think that they are already normalized. When I open txt file in R studio, I can have RPKM, P value, log fold change and base mean and other specifications. I am …

heatmap r studio log2foldchange

updated 5.9 years ago • alirezabcsaeidi

I recently downloaded a XML file of all the gene sets from MSigDB v7.2 from `https://data.broadinstitute.org/gsea-msigdb/msigdb...msigdb_v7.2.xml") Error: 'getBroadSets' failed to create gene sets: invalid BroadCollection category: 'c8' ``` When I try to import XML files from an older version (e.g. v5.2 -- which doesn't have the `c8` category) I get no errors. Is

GSEABase

updated 5.1 years ago • Ezgi

Otto <georg.otto at="" tuebingen.mpg.de=""> > Subject: [BioC] error in limma read.maimages(files, source="imagene") > To: bioconductor at stat.math.ethz.ch > > Hi, > > I am working with two-colour data generated by Imagene...gt;> myfun<-function(x) as.numeric(x[, "Flag"] < 1) >> RG<-read.maimages(files, sour…

limma limma

updated 19.9 years ago • Gordon Smyth

but, as far as I understand, they require a microarray experiment as input (or at least fold changes and pvalues). Since this time around I'm not starting from a microarray experiment but I just have a gene list, I'm looking...analysis using a simple numerical method such as Fisher's / hypergeometric test. I know the Category package still provides a KEGGHyperG class (which would be perfect!), …

Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools

updated 12.3 years ago • enricoferrero

div class="preformatted">Hello, since recently there's the affy package offers the mas5calls fucntion to get the P, A or M calls for a summarized probeset. The usual...but it could also be after normalization or even after pm correct. I'd be interested in your comments. I'm currently processing some chips from different experimental batches that have (depending on the batch) a shift...chip …

affy affy

updated 22.2 years ago • Arne.Muller@aventis.com

ago when no code was available). Which is not to say it did well then, or reflects any subsequent changes in dChip since then. Henrik is correct in that the pre-processing will also have an effect on your comparison. Although...I think recent versions of dChip do provide a quantile normalization implementation it is not the default, but the description...gt; > > > James, &am…

Normalization Preprocessing probe affy Normalization Preprocessing probe affy

updated 19.0 years ago • Ben Bolstad

div class="preformatted">Dear Seraya, Wei Shi has put his finger on the issue in a recent reply to this thread. Let me elaborate. Firstly, the true fold change for a gene expressed in one condition but not the...when a gene is absent in one condition, and has average expression value x in the other, the fold changes is computed something like: logFC = log2( (x+16) / (0+16) ) This means …

Preprocessing limma Preprocessing limma

updated 14.8 years ago • Gordon Smyth

Hi, I want to use pathview to show changes in certain enriched KEGG pathways. The range of the log2FC in the comparisons is rather different. Therefore the...Hi, I want to use pathview to show changes in certain enriched KEGG pathways. The range of the log2FC in the comparisons is rather different. Therefore the pseudocoloring...makes it hard to interpret the graph. Is there a (simp…

pathview

updated 5.1 years ago • da.de

div class="preformatted">Hi, I have a problem with my heat maps. I have a matrix of 222x2 of GO categories. I am using the heatmap.2 package to output an image. either a png or pdf. My problem is that the labels on the x axis...be able to differentiate between the single lables. But I didn't find how to do it. I tried to change the par(mar = c(3, 3, 2, 5), oma = c(3,2,2,6)) and also to …

GO GO

updated 14.8 years ago • Assa Yeroslaviz

this result? How can I fix it? Is it that I got too many genes which locate in almost all kinds of category so that there is no statistical significant enriched terms? Thank you in advance. --------- Edited: 2020-06-11 Thanks to the...comment by Kevin Blighe. I will show more information below. The `Acan.OrgDb` is the one I loaded by using Annotationhub, because...Although there are 691 …

clusterprofiler GO

updated 5.6 years ago • Ruixuan

true?) picture. I'm not the most knowledgeable in biochem but with mRNA c.2% total RNA, then a 2% change in rRNA and tRNA levels seems more likely than a 100% change in mRNA. Why not just measure mRNA/total RNA in the original...but doesn't have (the presumed) troubles discussed above. Obviously if you get a large number of changes biased in one direction then there would be a corresponding group…

Microarray Normalization affy limma gcrma Microarray Normalization affy limma gcrma

updated 21.3 years ago • Matthew Hannah

Hello I want to clarify the results I see under the log2 fold change column of the significantly differentially expressed genes table generated by DESeq2. If a gene for example has a...Hello I want to clarify the results I see under the log2 fold change column of the significantly differentially expressed genes table generated by DESeq2. If a gene for example has...log2 fold change of 6. Do…

DESeq2

updated 4.2 years ago • adeler001

new Ensembl marts for release 92 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: <pre> ensembl_mart_92 <- useEnsembl(biomart=“ensembl")</pre> You can find the complete...list of the changes at <http://www.ensembl.org/info/website/news.html

biomart ensembl release ensembl92 News

updated 7.7 years ago • Thomas Maurel

using a package called GO.db which is part of bioconductor, along the way I needed to find out the source of the GO ontology used by GO.db. As far as I an tell based on the package source, GO.db is relying on bioconductor to provide

GO ontology GO.db

updated 7.3 years ago • marcinjoachimiak

Is there any indication that the new labelling kit will lead to better overlall data, or is the change primarily intended to make the PM-MM measures more attractive? -francois ----- Original Message ----- From: "Matthew Hannah" <hannah...stat.math.ethz.ch> Sent: Wednesday, September 08, 2004 9:26 AM Subject: [BioC] Affymetrix is changing its labelling kit - data analysiswill change!? &am…

affy affy

updated 21.4 years ago • Francois Collin

makecdf using files supplied by Affy for their Rat Gene ST array. It does not seem to work with the Category package as it does not seem to have GO information incorporated. Output with some debugging info is below. Far below...is the script I used to generate the Gene ST package. [1] "beginning Category analysis" Loading required package: ragene10stv1.cdf.db Error in get(mapName, envir = pkgEnv…

GO cdf affy limma Category GO cdf affy limma Category

updated 17.2 years ago • Mark W Kimpel

<div class="preformatted">Dear R helpers, I'm a starter in gene expression analysis, and I must apologize everyone in the first place if I'm posting something irritated. My attemp is just to figure out an alternative way to find out differentailly expressed genes in low replicated datasets. In case that, I have very few number of replicated datasets per group (2-3 replicates per group). I…

updated 11.5 years ago • Guest User

He had 2 good suggestions: 1. Combine the two batch variables into one, if 3-4 reps are left in each batch 2. Use ComBat twice, adjusting for the first batch using the second batch as a covariate, and then adjust for...I cannot go with the first suggestion because combining the 2 batch variables would create 18 batch categories (3 batches * 6 rows), and I would not have enough replic…

GO Category sva GO Category sva

updated 11.9 years ago • Magda Price

are two questions: 1) Why does the distribution of the volcano plot skew so bizarrely to the left when I analyzed all 16 samples together, which was not the case when I analyzed only samples from a single patients versus

deseq2

updated 7.0 years ago • W. Gi

new Ensembl marts for release 93 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: <pre> ensembl_mart_93 <- useEnsembl(biomart=“ensembl")</pre> You can find the complete...list of the changes at <http://www.ensembl.org/info/website/news.html> Thanks, Amonida

ensembl mart ensembl93 biomart news News

updated 7.5 years ago • amonida

Wolfgang Huber <huber at="" ebi.ac.uk=""> writes: > ... this seems to have crept in recently. my first guess would be it has > to do with either Biobase or methods; for example: This seems to be related to a recent...change in R. We are investigating and will have a fix by tomorrow. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer

Cancer Biobase Cancer Biobase

updated 18.4 years ago • Seth Falcon

div class="preformatted">The data input for kooperberg() has been changed (greatly simplified). The function now accepts an RGList object. Reading either the documentation help("kooperberg...or the limma changelog would have told you of this change. Gordon > Date: Wed, 26 Oct 2005 17:28:40 US/Arizona > From: scholz at Ag.arizona.edu > Subject: [BioC] bioconductor 1.7...…

updated 20.2 years ago • Gordon Smyth

<div class="preformatted">Hi Gary- The plot should appear in the lower-left pane, which has tabs for Files, Plots, Packages, etc. I see in the screenshot that the pane is there and set to Plots, but it may be too small to show the plot -- you can try making the console pane smaller to enlarge the plot pane. I also see that you are using a somewhat dated version of R and hence of the DiffB…

DiffBind DiffBind

updated 11.6 years ago • Rory Stark

Hello, I'm looking for the source tar balls for these specific versions of IRanges, S4Vectors  and XVector. It looks like Bioconductor 3.4...Hello, I'm looking for the source tar balls for these specific versions of IRanges, S4Vectors  and XVector. It looks like Bioconductor 3.4 has...the updated versions of these. I looked in various places for the source - …

bioconductor iranges s4vectors xvector r 3.3.2

updated 7.5 years ago • chokoiboko

PValue FDR RMRP 2.802567464 2.802628518 11.43969321 1.94E-06 2.07E-05</pre> For Fold change > 5 and FDR < 0.05 <pre> tr <- glmTreat(fit, contrast=contrast.matrix, lfc=log2(5)) tab2 <- topTags(tr,n=Inf, adjust.method...PValue FDR RMRP 2.802567464 2.802628518 11.43969321 0.05563776 0.9930597</pre> But with Fold change > 5 and F…

edgeR r bioconductor diffferential expression fdr

updated 7.6 years ago • Biologist

Hi, Im new to using bioconductor packages in R, I'm importing .csv files into R for DeSeq2 analysis but I can't seem to get the first column of my colData to match the column names of my countData. The match (vector 1, vector 2) function isn't working and I think it has to do with the layout of my data. The image on the left is my table and the one on the right is an example of the requi…

deseq2 bioconductor

updated 6.9 years ago • ishtarredman

attributes (e.g. exon count) and get average exon count for genes in the different top level GO categories (1 step below the MF, BP and CC top domain). After reading the maillists, vignettes and googling around I'm still baffled

GO graph biomaRt GO graph biomaRt

updated 18.4 years ago • Palle Villesen BiRC

separate object) where I want. I made the legend like this : ```r lgd = Legend(title = "Log 2 fold-change", col_fun = colorRamp2(c(-3, 0, +3), c("#00aba9", "white", "#ff0097")),at = seq(-4,+4,by=2)) lgd2=Legend(title="Gene type",labels = c("protein-coding", "non...width = 40, height = 345,onefile = FALSE) draw(tryout, heatmap_legend_list = pd,heatmap_legend_side = "left") dev.off() ``` Whic…

ComplexHeatmap

updated 7 months ago • caroline.zanchi

Ensembl marts for release 100 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensemblmart100 <- useEnsembl(biomart=“ensembl") Please note that one vertebrate...name changed this release: old BiomaRt species name New BiomaRt species name cfamiliaris clfamiliaris

biomart ensembl e100 mart news News

updated 5.7 years ago • Thomas Maurel

Unfortunately, I found neither in edger manual nor in edger paper the description how the log fold change is calculated. Especially how those values <1 are treated because for instance, the log2 fold change of (0.7/0.03...is  4.544321 what is quite high log2 fold change but it resulted by dividing with a small number. How are the low normalized counts are treated…

edger normalization logfc

updated 10.0 years ago • tonja.r

Question: is there a way to test: (E_t2 - E_t1) ~ (Q_t2 - Q_t1) ??? We would like to know if the change in Q is associated with the change in E. Could help me design an equation in DESeq2 for that? Thank you very much in advance

Transcriptomics ExpressionData DESeq2

updated 2.7 years ago • Ivan

Hi, I read some previous posts and learned that it is statistically not really valid to filter results based on fold change (padj<0.05), for example only DEGs above/below 1.5 as this "flavours" lowly-expressed genes. Instead we should use lfc argument if we want to filter for fold change. I also learned that lfcShrink can be used to try and correct unreliable fold changes. Now my questio…

DESeq2

updated 4.8 years ago • zao.liun95

Dear List, Our sequencing core recently switched from STAR to Kallisto. The genewise output was given as both TPM values and counts. Gordon Smyth has written...that TPMs should not be used as input to EdgeR. In a recent paper (F1000 Research 2016,4:1521) Soneson, Love, and Robinson have presented evidence that the method they call simplesum_avextl...of-transcripts is as good or better for dif…

RNASeq-quantification edgeR TPM

updated 6.9 years ago • raf4

I'd like to resize the genes so that the range starts 500bp downstream from the current TSS without changing the end location. I've been looking at the resize and related functions, but can't figure out how to only change the start...and not change the end. Is this possible? Thanks

genomicranges

updated 10.8 years ago • Jake

For the past month the gradient colors of the Dotplot following EnrichGO (clusterProfiler) have changed. Instead of bright red to blue/purple, its pale red/ orange and strange blue. I didn't change the code, just using the standard

clusterProfiler

updated 2.2 years ago • inna.gur

normalisations assume that the different samples are similar, with the majority of probesets not changing. So the question is what to do when lots of them are changing due to different tissues, timepoints or treatments. I guess...then you get a lower correlation between replicates than if you normalise the 2 tissues separately. Recently a large dataset has become available which in parallel off…

oligo oligo

updated 21.5 years ago • Matthew Hannah

Dear all, In the vignette of GAGE pathway analysis package, a joint workflow with DESeq2 is shown, where only the column of log2 fold change from DESeq2 output is used as an input for GAGE. Is rlog matrix calculated by DESeq2 applicable as an input for GAGE pathway...pathway analysis package, a joint workflow with DESeq2 is shown, where only the column of log2 fold change from DESeq2 output is …

deseq2 gage

updated 9.5 years ago • Tom

error: __package or namespace load failed for ‘GO.db’__ Additional error message fall into two categories: 1. call: NULL   error: C stack usage  7970996 is too close to the limit 2.   call: NULL   error: evaluation...in an interactive session. Increasing  the stack limit (ulimit) for the shell session does not change the behavior…

package updates

updated 8.4 years ago • gctromp

<div class="preformatted">Dear List, I have used the genefilter package to filter out uninformative probe sets from my GCRMA normalised affy experiment as follows. f1 <- kOverA(3,6) f2 <- function(x) (IQR(x) > 0.5) ff<-filterfun(f1,f2) wh<-genefilter(esetGCRMA, ff) mySubSet<-esetGCRMA[wh,] I would also like to filter out those genes that have les…

genefilter affy gcrma genefilter affy gcrma

updated 19.9 years ago • Quentin Anstee

Hello, unfortunately, I cannot install packages into my library under C:R/R-4.2.2/library. If I reply no to the question ' Do you want to install from sources the package which needs compilation?" then it does temporarily download (ex. C:\Users\MY_UNDER_NAME\AppData\Local\Temp...my library under C:R/R-4.2.2/library. If I reply no to the question ' Do you want to install from sources the pac…

Install

updated 3.1 years ago • 무선

maintainers bump the development versions? I'm not sure if this has been fixed in Biobase, but the comment in zzz.R seems to indicate that's the original source of the code. Thanks, Cyrus</div

Biobase Biobase

updated 20.7 years ago • Cyrus Harmon

Dear.. I am looking for the MEDIPS bioconductor source code for the <span style="background-color:white">MEDIPS.couplingVector function (and any other MEDIPS source code

medips bioconductor error source code

updated 11.1 years ago • malbert1

I’m using a .ipynb notebook as source for my Vignette, so I created a Vignette engine inside my package to build it. That one registers a the necessary extensions...I’m using a .ipynb notebook as source for my Vignette, so I created a Vignette engine inside my package to build it. That one registers a the necessary extensions, and R CMD build obediently creates a vignette from the .ipynb file. …

package bioconductor bioc-devel developers

updated 10.6 years ago • flying-sheep

write some long R script. Does anyone can recommend some good examples on Bioconductor to read its source code? So I can learn how to write long R script more quickly in R's way. Thank you very much in advance. </div

updated 13.7 years ago • Fabrice Tourre

div class="preformatted">Hi all, I recently updated to R 2.8. I have a list of significant genes and want to do hypergeometric test to check for over-representing...oddsRatios, expectedCounts, catToGeneId > str(params) Formal class 'KEGGHyperGParams' [package "Category"] with 8 slots ..@ geneIds : chr [1:394] "3608" "8882" "9948" "163" ... ..@ universeGeneIds : chr(0)…

Annotation GO hgu133a2 hgu133plus2 Annotation GO hgu133a2 hgu133plus2

updated 16.9 years ago • Mayte Suarez-Farinas

coloring within plotCtCategory. > In especially, if in a sample there are not all the three categories "OK", > "Undetermined" and "Unreliable" but only let's say "OK" and "Unreliable", > the (default) colors for this sample show...and > red instead of green and yellow. The problem seems related to the > conversion of the categories to factor levels - in the abse…

Category HTqPCR Category HTqPCR

updated 14.6 years ago • Heidi Dvinge

gt; myfun<-function(x) as.numeric(x[, "Flag"] < 1) > RG<-read.maimages(files, source="imagene", path=file.path, wt.fun=myfun) Error in read.maimages(files, source = "imagene", path = file.path, wt.fun = myfun) : targets

limma limma

updated 19.9 years ago • Georg Otto

Bioconductor 3.1. When I am running the command to install BSgenome.Hsapiens.UCSC.hg19. <pre> source("http://bioconductor.org/biocLite.R") biocLite("BSgenome.Hsapiens.UCSC.hg19")</pre>   Error occurs:   <pre> Warning...recursive = TRUE, ...) : cannot create dir 'BSgenome.Hsapiens.UCSC.hg19/man', reason 'No space left on device' Error in myd…

bsgenome software error

updated 10.6 years ago • ltian

TRUE) When I plot this on a volcano plot, will genes that have significantly higher fold changes in the B group be on the right or left side of the plot? I'm a little confused by the documentation for `contrast`. Any help

deseq2

updated 5.8 years ago • gpreising

ordered following the time-series, i.e. 24hr and 48 hr on the right, and 6hr, 12hr, and 18hr on the left. In addition, how can I enlarge the text size, i.e. 0h, 6hr, 12hr, 18hr, 24hr, 48hr, and Condition? May I change the color for each Condition

diffbind

updated 10.5 years ago • Gary

interface to help. Type 'q()' to quit R. \[R.app GUI 1.66 (6996) x86\_64-apple-darwin13.4.0\] \[History restored from /Users/victor.trevino/.Rapp.history\] > source("http://bioconductor.org/workflows.R") Bioconductor...3.2 Warning message: package ‘rnaseqGene’ is not available (for R version 3.2.2)  > source("http://bioconductor.org/workflows.R") Biocon…

rnaseqGene genomic sequencing

updated 10.2 years ago • virctoalgn

of class '"ANY"': If the test method > supports it, can be used to specify a subset of category ids > to include in the test instead of all possible category ids. > > I don't know which test method supports this...Hence, reducing the set of GO IDs tested could remove some gene IDs from the universe and that will change the results for all tests. …

Annotation GO Cancer Annotation GO Cancer

updated 18.8 years ago • Seth Falcon

t identify which part of the text does this. However I am quite happy to have the clustering (of GO categories) but would like to be able to query the groupings to find insights into how it is clustered. Are these clusters named...I am using. GO<-read.delim("file.txt",header=TRUE) GO GO[,-c(1)] row.names(GO)<-GO$NAMES source("http://www.bioconductor.org/biocLite.R") biocLite("ALL")…

Clustering Clustering

updated 15.3 years ago • Elizabeth Ashley

div class="preformatted">Hi, In boxplot(), is there a simple way to change the box colours for varifying no. of columns. In a different attempt, I could do the change of colour, for say, after every

updated 16.1 years ago • Chintanu

i have 1000 genes obtained from the comparison 1 (A vs B) and i would like to obtain the Fold Change and pvalue of this 1000 genes in the comparison 2 (C vs B). After that what i'm gonna to do is to obtain a sort of "value" in order...to estimate the "% change" of each gene from the comparison 2 respect the comparison 1 and i don't think that comparing the FC (experiment A) with...the FC (experi…

updated 14.5 years ago • Alberto Goldoni