User: thokall

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thokall100
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Swedish Museum of Natural History
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Posts by thokall

<prev • 19 results • page 1 of 2 • next >
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Answer: A: The query to the BioMart webservice returned an invalid result: the number of co
... There appear to some issues with the release of ensembl ver. 91 some days ago perhaps your problem is related to this. See for example: https://support.bioconductor.org/p/104025/#104121 So try to to either install a patched version via GitHub BiocInstaller::biocLite('grimbough/biomaRt') and load the ...
written 10 weeks ago by thokall100
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Comment: C: Ensembl 91 is out!
... There were some issues with the new release so if you have issues check this out   ...
written 10 weeks ago by thokall100
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Comment: C: biomaRt: drerio_gene_ensembl dataset missing
... You could instead of using an old archived version go for version 90 from August (http://Aug2017.archive.ensembl.org), which in many cases will have limited differences to the very latest release ...
written 10 weeks ago by thokall100
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Comment: C: biomaRt: drerio_gene_ensembl dataset missing
... The same issue was happening also yesterday. It is still likely due to the update at ensembl, but it is suboptimal that the default behaviour of useMart() uses an not yet complete instance and does in addition not generate any warnings   ...
written 10 weeks ago by thokall100
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Answer: A: How to convert Illumina HT_12_v4 annotation
... Hi, There are certainly ways of doing this from R using bioconductor packages. If you start by importing your data into R you can then use the annotation package "illuminaHumanv4.db" to convert illumina probe names to other identifiers. # install the package source("https://bioconductor.org/biocL ...
written 10 weeks ago by thokall100
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Comment: C: RNA-Seq : zero counts
... Hi, Have you checked that the chromosome names in your bam files corresponds to the annotations you are using? If there is mismatches in chromosome name between annotations and bams (most often either 1 or chr1 for chromosome 1) you might get 0 counts. ...
written 12 weeks ago by thokall100
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Comment: C: Reference annotation file contains only transcript and CDS information, how to a
... Hi, Not sure this questions fits this forum as it is not directly related to bioconductor. You are more likely to receive help if you post names of the actual packages in bioconductor that you are trying to use or if it is a non-bioconductor question turn to biostars or other more general bioinform ...
written 3 months ago by thokall100
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Comment: C: Basic doubt about the program
... Hi, Note that this is a forum for getting help with questions related to bioconductor packages. If you want help with a specific bioconductor package please state explicitly which package you are trying to use and add information on exactly what you want help with ...
written 3 months ago by thokall100
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Answer: A: KEGG with pathview using CuffDiff data
... Hi, You need to map your gene ids to KEGG pathways, but without knowing what gene id you have in your data it is hard to point you in the right direction. If you are in a model species you can retain gene names from the GTF file by adding -g or -G to you cufflinks command. Note that cufflinks is no ...
written 3 months ago by thokall100
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Comment: C: GSEA using clusterProfiler
... Hi, It seems that you have the same issue as in your previous question regarding clusterProfiler. Have you checked that your supplied gene list of the right type and from the right species? It would be helpful if you also showed the output of the function: >head(geneList) Regarding the TERM2G ...
written 3 months ago by thokall100

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