User: thokall

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thokall60
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Posts by thokall

<prev • 13 results • page 1 of 2 • next >
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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 4 days ago by thokall60
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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 4 days ago by thokall60
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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 7 days ago by thokall60
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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 14 days ago by thokall60
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Answer: A: question on GO analysis using clusterProfiler
... Hi, Please try and clarify exactly what you have done. Your initial gene list does indeed as stated by  Guangchuang Yu contain human geneIDs so they will not map to mouse. The code you supply work with mouse gene ids. The example below is your code and part of your example data, but adding a mouse ...
written 14 days ago by thokall60
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Comment: C: queries reg limma
... Hi, What have you tried so far and what goals do you have? I would encourage to read the Limma vignette and check chapter "3.2 Sample limma Session" that have some basic information on how to import and analyse gpr files. ...
written 15 days ago by thokall60
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Comment: C: question on GO analysis using clusterProfiler
... Hi, It looks like there might be some issues with your input, but it is not possible to offer a solution without knowing the content of your geneList object. In addition with the code you show the same content [names(geneList)] is given to argument 'gene' and argument 'universe' in the enrichGO fu ...
written 16 days ago by thokall60
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Comment: C: Volcano Plot (highlighting top genes in a different color)
... If you followed the example by Turner you, the data frame res have a column with the name Gene.  > head(res)      Gene log2FoldChange    pvalue      padj 1    DOK6         0.5100 1.861e-08 0.0003053 2    TBX5        -2.1290 5.655e-08 0.0004191 3 SLC32A1         0.9003 7.664e-08 0.0004191 4  IFI ...
written 17 days ago by thokall60
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Answer: A: Volcano Plot (highlighting top genes in a different color)
... Hi, Not sure exactly what you mean, but looking at the first example you can identify the threshold for fold change and then almost unaltered use Turners example. threshold.high <- sort(res$log2FoldChange, decreasing = TRUE)[20] threshold.low <- sort(res$log2FoldChange, decreasing = FALSE)[ ...
written 17 days ago by thokall60
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Comment: C: Adding gene names which are differentially expressed in the plot
... So a scatterplot with what values? Two common types are volcano plots and MA plots. You would likely get faster and more useful answers if you add the code snippets you tried so far and perhaps a link to an example of a figure that you would like to create. ...
written 19 days ago by thokall60

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