User: MAPK

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MAPK0
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Posts by MAPK

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Submitting R package in Bioconductor with Plink and vcftools Dependencies
... Hi All, I have written a program to analyze genotype SNP data in R and wanted to submit it as a bioconductor package. However, this package will be using Plink and vcftools and I was wondering if it is possible to submit it with such dependencies. Can someone please guide me though what I need to do ...
R package dependencies written 3 months ago by MAPK0 • updated 3 months ago by Aaron Lun24k
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Comment: C: Help with multi-factor Deseq analysis
... Thanks Michael. I merged `cond` dataframe as you suggested, but got the following error below. How do I reduce for one column factor? Could you please confirm if I am doing it correctly? cond$TimeTreatmentCultivar<- as.factor(paste(cond$cultivar,cond$time,cond$treatment, sep = "_"))     dds < ...
written 10 months ago by MAPK0
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Comment: C: Help with multi-factor Deseq analysis
... Thanks, Michael. I got these results below. Now, how do I run contrast for 1 to 4 ? Could you please confirm if it's correct what I have below? Yes for 5, I just want to see the overall effect.   cond$CultivarTreatment <- paste(cond$cultivar, cond$treatment, sep="_") head(cond) cultivar tim ...
written 10 months ago by MAPK0
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Help with multi-factor Deseq analysis
... Hi All, I need help to resolve this problem with deseq. I have two  cultivars (`R` and `S`), two time points (`5d` and `30d`) and four treatments (`Scn`, `Aph`, `ScnAph`, `Ctr`). There are two sets of controls (`Ctr`) for each cultivar and I have a total of 48 samples.  I need to compare:  1. Scn V ...
rnaseq deseq deseq2 written 10 months ago by MAPK0 • updated 10 months ago by Michael Love24k

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