User: thokall

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thokall110
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110
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Location:
Swedish Museum of Natural History
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nucdiv
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Google Scholar Page
Last seen:
13 hours ago
Joined:
6 months, 3 weeks ago
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t******@me.com

Posts by thokall

<prev • 22 results • page 1 of 3 • next >
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Comment: C: how to create csv file with name of gene from unique ID of lcpm ?
... If you in an interactive r session do your analysis and type y2$genes you will see that this is not a vector. You hence have to select one of the columns (= a vector) of this dataframe to use as row names. ...
written 4 weeks ago by thokall110
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Comment: C: use deseq2 in asthma
... You will likely get better answers if you show the code you have tried so far and the errors that it generates. If you mean the package Genomicfeatures you should be able to follow the instructions at https://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html ...
written 4 weeks ago by thokall110
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Answer: A: package DESeq2 installation with R.
... DESeq2 is part of bioconductor and can be Installed according to the instructions that you find here https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html ...
written 10 weeks ago by thokall110
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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 5 months ago by thokall110
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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 5 months ago by thokall110
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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 5 months ago by thokall110
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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 5 months ago by thokall110
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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 5 months ago by thokall110
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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 5 months ago by thokall110
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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 6 months ago by thokall110

Latest awards to thokall

Scholar 6 months ago, created an answer that has been accepted. For A: Using R for EnrichR analysis
Scholar 6 months ago, created an answer that has been accepted. For A: Volcano Plot (highlighting top genes in a different color)

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