User: theobroma22

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theobroma221.1k
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Posts by theobroma22

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Answer: A: Limma design and makeContrasts
... An alternative would be to get the normalized expression values of each group. This way you can do a lot more in terms of analysis with the datasets, in addition to determining the DEGs. At the end of your program, see how the below code may help you : vfit <- lmFit(v, design) efit &l ...
written 12 weeks ago by theobroma221.1k
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Comment: C: Learning community for newbies
... I’ve been in this field for more than 5 years and have learned a lot but always feel like I’m just starting the journey - maybe because I’ll always be a student. In my humble opinion Biostars IS the ideal place because peoples’ experiences are so broad - this way, I not only learn, but also teach! ...
written 12 weeks ago by theobroma221.1k
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Comment: C: Determining efficient solvents for extracting metabolites
... This might be found in reference books; like acetone is a very very strong solvent. ...
written 3 months ago by theobroma221.1k
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Comment: C: Determining efficient solvents for extracting metabolites
... Water is polar, and Chloroform and methanol are non-polar. ...
written 3 months ago by theobroma221.1k
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Answer: C: merge table with gene ID and names
... Try: `result <- merge(t1, t2, by.x = "geneID", by.y = "respectivegenename", all = TRUE)` The native gene IDs may be listed after the "respectivegenenames". ...
written 3 months ago by theobroma221.1k • updated 3 months ago by zx87544.5k
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Comment: C: Error while using EdgeR
... Do you have NAs or Infs in your matrix? How did you normalize your data? ...
written 3 months ago by theobroma221.1k
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Comment: C: Most genes with entrez id in KEGG database don't have a pathway assigned. Is the
... I’m not sure of any method to do that. I do find genes that are not assigned, or curated, to pathways are mostly oxidation-reduction related genes. You could search NCBI or Uniprot to see if there is any curation outside of KEGG. Alternatively, a gene enrichment analysis might be helpful, but again ...
written 3 months ago by theobroma221.1k
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Answer: A: How to apply GenVisR Bioconductor package on VCF file
... The input to waterfall consists of a data frame derived from either a .maf (version 2.4) file or a file in MGI annotation format (obtained from The Genome Modeling System) specified via the fileType parameter. https://bioconductor.org/packages/release/bioc/vignettes/GenVisR/inst/doc/GenVisR_int ...
written 3 months ago by theobroma221.1k
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Answer: A: Phenotype data analysis for QTL validation
... That’s a good place to start. Doing this will help to know which parts of the model you can possibly drop or new terms to include in a new and different model. ...
written 4 months ago by theobroma221.1k
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Answer: A: boxplot in edgeR
... Try mean-centering your data with the log scale transformation. ...
written 4 months ago by theobroma221.1k

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