22,183 results • Page 1 of 370
Input file is the list of gene ids along with fold change values: ``` 14 1.23 43 -1.18 52 1.42 90 -1.2 212 1.42 291 -1.11 337 1.29 351 -1.31 358 1.19 372 -1.5 411 -1.43...1.13 471 -1.24 585 -1.46 596 -1.47 607 -1.47 632 1.37 ``` Column one is gene id and column 2 is fold change Code having error is: ```…
updated 3.4 years ago • Safina
div class="preformatted">Dear Zhe, To do clustering of RNA-seq profiles using the edgeR packages, you can use the plotMDS.dge function. See the User's Guide for examples...This function is already designed for RNA-seq data, so there is no need to worry about normalization factors or variance stabilizing transformations etc. Best wishes Gordon [BioC] edgeR...Hello, I have a question about …
I am attempting to use enrichGO in clusterProfiler to identify gene ontologies for three gene clusters (diff_genes) relative to the full set of 7000 genes (all_genes). I am getting a warning...no genes can be mapped' that appears to relate to the format of the locus linked IDs. However, I have removed any IDs that are of...my genes are simply not in org.At.tair.db, but this seems surprising for a…
I am trying to use clusterprofiler to enrich the pathways in my datasets. But I am getting the error "No gene can be mapped". Any insight will be really helpful. Thanks <pre> &gt; require(clusterProfiler) Loading required package...rawdata&lt;- read.delim("tobacco",header=TRUE,check.names=FALSE) &gt; head(rawdata) Pathway Gene 1 map00010 K00001 2 map0…
updated 7.2 years ago • prp291
Hi there, I have am getting different outputs after running enrichGO on cluster profiler when I put the same genes into enrichR (by Maayan Lab) website. Example here using Biological Process 2021...lt;- marker.gene.clust[[i]][marker.gene.clust[[i]]$summary.logFC&gt;1.5,] #print(markerFile) gene &lt;- marker.gene.clust.filt$Symbol gene.df &lt;- bitr(gene, fromT…
updated 2.1 years ago • angkoo
Hi, I identified DEGs with LRT test in DESeq2 and clustered them with degPatterns. There were 78 DEGs but 48 genes were clustered by degPatterns. And all 48 DEGs were clustered...into cluster 5 and 6. But why there was no gene in cluster 1-4? And the plots only shows cluster 5 and 6. If the 48 genes can only clustered...gt;% data.frame() %&gt;% rownames_to_column(var="gene") %&gt;%…
updated 5.0 years ago • lqsdau
div class="preformatted">Hi all, I want to cluster some genes based on their GO term annotation information in Arabidopsis and plot the profile. I tried some packages...in Bioconductor including 'goProfiles', 'org.Hs.eg.db', but it says "No ancestors found for this GOTermsList ". The code I tested is as follows: ---------------------- require(goProfiles) require(org.At.tair.db) #first...map…
The OrgDb should be Salmo salar, but I did not found this in the reference. enrichGO(gene, OrgDb="org.Dr.eg.db", keyType = "ENTREZID", ont = "BP", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize...10, maxGSSize = 500, readable = FALSE, pool = FALSE) Results: &gt; --&gt; No gene can be mapped.... &gt; -…
updated 3.2 years ago • Carolina
I believe bioconductor must have some solution for that.) Is there a guideline or good tool to get "gene" expression profile from "probe" expression profile? In this process, I am concerned that such tool or guide should address...the issues of "multiple probes to one gene" and "one probe to multiple genes". I believe it is a non-trivial process and automation of this process might not be easy…
updated 17.0 years ago • Weiwei Shi
term2gene, TERM2NAME = term2name) preparing geneSet collections... --&gt; Expected input gene ID: 130632269,130647644,130636300,130646236,130614559,130655215 Error in check_gene_id(geneList, geneSets) : --&gt; No gene...can be mapped.... head(term2gene) GO_ID GeneID 1 GO:0004930 130612030 2 GO:0007186 130612030 3 GO:0016020 130612030 4 GO:0004799 130612032
updated 8 weeks ago • nromerov
<div class="preformatted">Dear list, I am trying to create Arabidopsis mappings from genes to Pfam- profiles, because these are not included in the default annotation package. Thus I have downloaded the mappings from IPI and generated a table with column1 the gene id and column 2 the Pfam profiles, and dropped this table into a SQLite-file (Pfam.sqlite) using the RSQLite package. In the e…
updated 15.8 years ago • Samuel Wuest
function of clusterprofiler for GO enrichment of my non-model organism. First I have my DE genes (n=638, converted as character): gene &lt;- read.csv("list.csv", header = F,sep=",") gene &lt;- as.character(gene[,1]) head(gene) [1] "BANY.1.2.t20473...alpha-1,6-mannosyltransferase activity Then run the program x &lt;- enricher(gene,TERM2GENE=term2gene,TE…
updated 4.0 years ago • tianshenbio
and sequenced them in 12 lanes, &gt; respectively. I want to see the similarity of the 12 samples by clustering and analyze DE between &gt; different species and between different species. Can I separate the 12 samples to 2...is yes. Best wishes Gordon &gt; Thanks, &gt; Zhe &gt; &gt; &gt; &gt; Dear Zhe, &gt; &gt; To do clustering of RNA-seq profiles using…
Hi all, I'm using clusterProfiler to check a list of genes for KEGG pathway enrichment. While that list of genes did not show any significant enrichment (as was expected), I was still...curious which pathways they mapped to. To figure this out, I set `pvalueCutoff=1` and `qvalueCutoff=1` assuming that the result should then show me all pathways...to which genes map. However, the analysis…
updated 22 months ago • michaelR
Hi there, I'm currently running cluster profiler and set my adj p value at &lt;0.05. The example below showed I have 3 terms that meet the threshold. However, when...Hi there, I'm currently running cluster profiler and set my adj p value at &lt;0.05. The example below showed I have 3 terms that meet the threshold. However, when I ran the same list of genes in Enrichr website, the p.…
updated 19 months ago • angkoo
having an error when I try to use clusterprofiler enricher feature for MsigDB analysis of a list of genes. I have been following the code here: https://yulab-smu.github.io/clusterProfiler-book/chapter3.html#msigdb-analysis...4.332800 3.822049 3.799207 I then defined the threshold for expression change: &gt; gene &lt;- names(geneList)[abs(geneList) &gt; 1.2] &gt; head(g…
updated 5.0 years ago • rm1238
preformatted">Dear list members, I'm an undergrad and I work in a lab at Brandeis. I am trying to cluster around 14,000 genes across 6 microarray experiments. Two of these experiments are replicates. I have decided to use...R since it seems to be the most complete and flexible software package for normalization and clustering of microarray data. The problem is that I am new to clustering
map the given entrez IDs. This issue first occured on my macOS running Jupyter Notebook. Even the genes and codes I used before, couldnt be mapped anymore. I first thought, it would be a problem with the R enviroment, maybe updated...pvalueCutoff=0.01) Reading KEGG annotation online: Reading KEGG annotation online:sue --&gt; No gene can be mapped.... --&gt; Expected input gene ID:…
updated 12 months ago • ckilian.cklab
for backwards compatibility more than anything else. This is why the man page for the ACCNUM mapping says this: "For chip packages such as this, the ACCNUM mapping comes directly from the manufacturer. This is different...from other mappings which are mapped onto the probes via an Entrez Gene identifier." Anyhow the code that builds the ChipDb package is...I get this output: &gt; &gt;…
updated 9.6 years ago • Marc Carlson
this sounds like a rather trivial question but somehow the an answer eludes me. I am analysing gene expression data with limma in a two-factor model with interactions. No problems there. What I would like to do is to first...cluster the genes (using my own clustering procedure that I'm working on), and then search for clusters that are differentially...expressed (e.g. factor A is significant in …
updated 10.4 years ago • January Weiner
sample data and used hcluster on my microarray arrays as in the following example. I subset on the genes and then cluster the arrays based on the genes of interest. I use Euclidean distance and average linking. Is this the same...between groups?Also, is there any reason to use PHYLIP to display the relationships of expression profiles instead of using hcluster or some other clustering algorithm? …
package can be loaded sh: line 1: 61860 Segmentation fault (core dumped) '/usr/lib64/R/bin/R' --no-save --slave 2&gt;&amp;1 &lt; '/tmp/Rtmp1c8RKq/filef19c7a7d05e9' *** caught segfault *** address (nil), cause 'memory not mapped' An irrecoverable...removing ‘/home/sato_y/R/3.4/DOSE’ *** caught segfault *** address (nil), cause 'memory not mapped' Traceback: 1: q("…
updated 5.8 years ago • heir_of_isildur88
everybody, I am using the Mfuzz package (v. 2.30.0) for analysing the effect of a time series on gene expression and I therefore manage to cluster the genes from this dataset, based on their expression profiles. I would...like to know how it is possible to actually identify which genes are part of each cluster, in order to export these lists and make some gene ontology analysis. Is it possible w…
updated 8.0 years ago • thomas.dobrenel
Dear all, given a set of ChIP-seq datasets, which package would you recommend for making meta-gene profiles ? Thanks, Bogdan
updated 2.1 years ago • Bogdan
gt; &gt;I have already analyzed these data using limma, just to have an idea of &gt;regulated genes at 6 hr and 24 hr, but now I would like to cluster the data &gt;across the time points to group the genes according to their...expression &gt;profile. &gt; &gt;My question is: what method should I use in order to do this? I have checked &gt;already the timecourse<http…
samples which are of differnet stages. The experiment was not properly designed for expression profiling but i wanted to extract some meaningful and correct information from the analysis I have the data set up like this...11) (50 million) The total reads for 5 diff stages varying from 30 million to 400 million. There is no reference genome for this so i assembled them using trinity by combining…
updated 11.2 years ago • empyrean999
I am trying to figure out why thousands of transcript clusters are not mapped in `` ragene20sttranscriptcluster.db `` while they are perfectly present in the manufacturer's materials...order/catalog/product/902124>), with chromosome coordinates given (chr1+:23093113-23164282), gene symbol (Enpp3), transcript ID (NM\_019370) etc. But in `` ragene20sttranscriptcluster.db `` this cluster is not m…
updated 5.6 years ago • aush
div class="preformatted">I would like advice about software and appropriate approaches for clustering genes. I have results from a series of 45 cDNA arrays comparing RNA sample extracted from a hela human cell line...to a reference. There are 3-4 replicate arrays for each transcription factor. I have classified each gene as likely up, down, neither for each transcription factor. Now I would l…
Greetings,&nbsp; SC3 provides an expression matrix after clustering genes&nbsp;by kmeans with k = 100. __How does one extract the cluster to which each gene was clustered?__ I checked...Oddly, the column sc3\_N\_markers\_clusts has numbers ranging from 1 to N, where N is the k used to cluster cells, not genes. I'm not sure how a gene can be discretely associated with a cell cluster and I…
updated 6.4 years ago • ahmed.elewa
Hi, Working with the Illumina Human WG6 chips, and lumiHumanAll.db. After linear model fitting and clustering, I have identified a cluster of ~130 loci that show an interesting profile. However, as 125 of them have no GeneName...gt;From a closer inspection of lumiHumanALl.db, I find that approx. half of the features have no EntrezID, so I wasn't just unlucky with the constituents of my cluster!…
updated 15.8 years ago • Al Ivens
Hello, I'm struggling with co-expression analysis, and for that I would like to try to cluster all the genes I have in my microarray set, including those which are not differentially expressed between the study...my luck with GSCA as well, but both packages seem to have been layed out for 3000 rather than 30000 genes. How do you do that in R? I get errors about R not being able to allocate enou…
updated 12.6 years ago • January Weiner
to ask if someone could give me a little overview of the options I have if I want to determine clusters of correlated genes in expression data. I have found several useful functions, but as usual, no matter how hard I look
updated 17.0 years ago • knaxerov@ix.urz.uni-heidelberg.de
belonging to approximately 6 different cancer subtypes. Essentially, I am hoping to first identify "gene modules" of gene expression corresponding to a specific cancer subtype, or groups of subtypes. (e.g. present only in A and...B cancer, but not in C, D, E or F). Subsequently, I wish to label these modules by gene ontology. (e.g. "T-cell response" module) I tried a non-R program (GenXpress) wh…
at a dataset comprised of Affy images from disease- affected tissue samples that I am trying to cluster. The problem is that we have 2+ biopsies per study subject, and I am not sure how to best account for their dependency...samples, these biopsies differ to a certain extent in their disease severity. I first tried to just cluster all available biopsies using ConsensusClusterPlus. However, this…
updated 10.8 years ago • Moritz Kebschull
and number of reads). It looks like that (\*image below). And I have to compare two coverage profiles of two samples. There are several methods to do that (Pearson correlation, Euclidean distance, Chi-square, t-test, clustering...is to validate the result. I have two samples (control and new) and I want to know that the coverage profile of new sample is the same with control sample. \*important …
the count matrix or table of read counts should be actual values representing total number of reads mapping to a gene. There are some genes with no reads mapping at all, hence have zero values for some samples, whereas for some...samples they have very high read counts. For these genes, the logFC values come out very high:- 144269492.898735 in my edgeR DE analysis. Is this correct? Regards, Can…
updated 9.2 years ago • candida.vaz
is plotted by syntenet (https://github.com/almeidasilvaf/syntenet) that visualizes the phylogenomic profiles for the different species and groups; What exactly are the different colors corresponding to increasing numbers...e.g. red color -&gt; +3)? In addition what does the clustering tree on top of the figure represent? Are these groups of clusters that are shared in different species? Some …
updated 16 months ago • Alexandros
and some others works related to Illumina microarrays but I'm still not sure if I have to use gene profile or probe profile files. What are the advantages or disadvantages of each one? Which one is the most adequate for
updated 10.7 years ago • Guest User
Dear all,&nbsp; I am running a differential gene expression between 2 groups and got 124 differentially expressed genes using the limma package.&nbsp; When I run hierarchal...clustering on the dataset using 30 top genes I get pretty clear separation between the 2 groups. When I increase the number...of genes to 50 the separation is not so clear and with 124 genes, I don't see the separa…
Hi everyone, I am analyzing the expression profile of about 12,000 genes, cluster analysis using &nbsp;fuzzy C-means by using Mfuzz package in R. However, whether I use a C...value of 100 or 50, for each cluster, I only got very few genes with a membership value higher than 0.7, say only 20 or 40 genes. There are still far too much...genes are not in the cluster. &nbsp;Has anyone ever me…
updated 8.8 years ago • Emily
Hi all, I have been trying to extract the GSEA results from a list of genes after RNAseq analysis. It looks like my gseKEGG function is giving me problems. I am unable to generate a list of KEGG...Hi all, I have been trying to extract the GSEA results from a list of genes after RNAseq analysis. It looks like my gseKEGG function is giving me problems. I am unable to generate a list of KEGG terms…
updated 13 months ago • redafazazi
package. I was able to understand the entire flow. But, I am having tough time gettting miRNA to Gene mapping. I got the predictions using "http://www.microrna.org/microrna/getDownloads.do", But the mapping does not exist...for my entire set of miRNAs. Please suggest me a source where I can obtain the miRNA to gene mapping. The platform used is for miRNA analysis is Agilent. Does anyone know if …
updated 10.0 years ago • Kishor Tappita
Hello! I have just run maSigPro's see.genes() function to obtain the graphical output for clustering. How do I then obtain lists of the genes that contributed to the different clusters? Thank you
updated 7.7 years ago • ls299
Hi everyone, I'm interested in generating a gene clustering similar to the one in this workflow: [RNA-seq workflow: gene-level exploratory analysis and differential expression...1] (see "Gene Clustering" section 6.3) I would like to do for the DESeq2 results only (ie the deferentially expressed genes determined...result would show the two **groups** that I've **compared** (eg. control and…
updated 4.0 years ago • Matan G.
div class="preformatted">Hi, I m currently trying to run some clustering on some expression arrays and I was wondering about the best way of doing it, I have 81 samples on hgu133plus2 (55000...down to approximately 10000 (X, Y, low variabilty, control probes), and wanted to try hierarchical clustering on these both by arrays and genes. I was planning on using hopach as this seems an easy and …
updated 15.7 years ago • Nathan Harmston
preformatted"> Hello, The following are the command lines that I have been using to filter out genes with small profile variance from gene expression data by Matlab. ---------------------------------------------------------------------- % filter genes with small profile variance % less than
updated 10.1 years ago • Jerry Cholo
Hi, I am interesting in clustering my single cell data to identify clusters and then figure out if certain genes differ in expression profiles and...then try to link them to developmental stages.&nbsp; 1. So, to be able to compare gene to gene expression, I suppose the expression scores should be corrected for gene length. Does SC3 do this somehow? I don...t pass in a gene length argument a…
analyze a time-series microarray data generated with Yeast 2.0 chip. There are 30 time-points with no replication. Is there any package I could you to: - identify genes with significant expression changes through the 30 points...cluster the significant genes and visualize the average expression profile in each cluster ?????? Thank you very much for any suggestion
updated 15.2 years ago • Paco Recca
edgeR analysis based on the padjustvalue lessthan 0.05 I chosen significantly expressed differential genes include both Up/Down regulated genes. I chosen, zebrafish annotation for my data, performed Gene Set enrichment analysis...works very well. While KEGG enrichment step I'm getting **"no term enriched under specific pvalueCutoff..."** any sugesstions ? In this case, how do I get KEGG ann…
updated 3.7 years ago • sunnykevin97
But for making alignment plots it is working ok. The package makes an effort to handle overlapping genes correctly and not to use feature data twice, etc. It's easy to make plots on 5' or 3' gene borders only, or on all borders together...alignments on gene subsets of different gene length is much more instructive. If you want to use it, even though it is under development, please...Dear BioC, &…
updated 14.1 years ago • Ludo Pagie
I want to use the groupGO function from cluster profiler, but do not exactly understand the `` level `` argument. The help page (hence `` ?groupGO) `` says: "Specific GO level." When...lt;- groupGO(gene = All_genes, keytype = "ENSEMBL", OrgDb = org.Hs.eg.db, ont = "BP", level = 3, readable = F) &gt; dim(as.data.frame(ggo_all)) [1] 585 5 &gt; ggo_all...lt;- groupGO(gene = All_genes, k…
updated 5.9 years ago • b.nota
I am trying to run pathview with expression data from potato RNAseq. My RNAseq was originally mapped on PGSC identifiers which I am able to convert into NCBI GeneID (Entrez) identifiers using gprofiler (https://biit.cs.ut.ee...pathviewdata, pathway.id = "04075", gene.idtype = "entrez", species = "sot", limit = list(gene = 7, cpd = 7), out.suffix = "test27") #Second trial using kegg as gene.idt…
I am running `affy::justRMA` function on a **computer cluster** to make expressionset from **HTA 2.0 CEL** files. The function runs fine when I run # part 1 of the code (see the **attachment...in the **attachment**) ![*** caught segfault *** address 0x2b3583efa830, cause 'memory not mapped'][1] Since I run this function on computer cluster I have `173GB of RAM` and as you may see fro…
Hi, I am using clusterProfiler to do an enrichment analysis. However, I get the warning ' No gene can be mapped.... --&gt; Expected input gene ID: ND6,ND4,COX3,ND1,ND5,ATP6 --&gt; return NULL...'. I am studying a non-model organism, the...ENTREZID"), OrgDb = Vulpes.OrgDb) genelist &lt;- df2$ENTREZID enrich.go.BP = enrichGO(gene =genelist, Or…
updated 18 months ago • yuhang
and then remove it.&nbsp; Since the voom+limma approach is shown to work well for differential gene expression, we thought of estimating the weights for each observation through voom and then use them in the limma function...the end we get log2(cpm) corrected for the batch (I guess?) and we get some biologically meaningful clustering.&nbsp; As a next step, we wanted to cluster genes bas…
quality of RNA extracted using Trizol from human PBMC and it was not so bad (RIN 7-9). I checked the profile of cRNA after IVT using One-cycle kit of Affymetrix and it peaked around 1000 nucleotides. Then I hybridized the human...or is it very low? When we performed the analysis (Limma), I could not find differentially expressed genes, I mean I found around 50 genes and I know this is not the cas…
updated 16.5 years ago • brini.elena@hsr.it
of Bioconductor annotation packages: Probe Id --&gt; refSeq Id / Unigene Id --&gt; Entrez Gene Id -- &gt; annotation At each step, the mapping could be missing. For example, for the whole-genome chips, about half of probe Id...lumi ID mapping packages provide mapping information of probe Ids to refSeq Ids. Lots of probe ids have no refseq id mapping available...due to the rea…
has 60778 mapped keys (of 103510 keys)" [8] "hugene10sttranscriptclusterCHR has 19962 mapped keys (of 33297 keys)" [9] "hugene10sttranscriptclusterCHRLENGTHS...has 93 mapped keys (of 93 keys)" [10] "hugene10sttranscriptclusterCHRLOC has 19424 mapped keys (of 33297 keys)" [11] "hugene10sttranscriptclusterCHRLOCEND...has 19424 mapped keys (of 33297 keys)" [12] "hugene10sttranscriptclusterENSEMB…
updated 9.6 years ago • Thomas Pfau
Hello, I want to enrich KEGG pathways on my rice genes. I tried "clusterProfiler", but its input is entrezID and my gene ids are RAPIDs (Os02g0617800). I want to keep using the RAPIDs...so I have to write my own enrichment functions. To do this, I need the mapping between RAPIDs and pathways. How to get the mapping from KEGGRSET? Regards
updated 5.1 years ago • zhang.jianhai
div class="preformatted">Hi There: I'm trying to cluster 13777 genes that are differentially expressed across three different treatments but I'm getting the following...I wonder how could I fix it in order to get the clusters and the heatmap with the expression profile. I would appreciate any suggestion from you!. Thank you so much for your
updated 14.0 years ago • avehna
22,183 results • Page 1 of 370
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