User: Ashastry

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Ashastry60
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Posts by Ashastry

<prev • 12 results • page 1 of 2 • next >
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Comment: C: devtools Installation error in R (version 3.5.3)?
... As suggested by Arup, start a new session and then do this - ` BiocManager::install("devtools")` ...
written 5 months ago by Ashastry60
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Answer: A: Statistics on differentially expressed genes
... Can you please elaborate on how you are planning to make a selection? I think most of the DE tools are designed to handle the entire dataset as it is for a better fit. You will be skewing the data if you are randomly filtering your genes with some cutoff. If you are planning on removing zero counts, ...
written 5 months ago by Ashastry60
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Comment: C: devtools Installation error in R (version 3.5.3)?
... What error did you receive when you tried to install biocLite? ...
written 5 months ago by Ashastry60
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Answer: A: devtools Installation error in R (version 3.5.3)?
... Can you try it with a different CRAN mirror? Also may be try this source("https://bioconductor.org/biocLite.R") biocLite("devtools") ...
written 5 months ago by Ashastry60 • updated 5 months ago by zx87548.2k
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Comment: C: Load phenotype data for samples
... Hi, Phenotype data file should explain the variables in your samples. Ideally it should either have a "condition" or other variable like "time point" depending on the design of your experiment. If you look at csv file from the data, it is clear that the first column consists of sample name/ID, se ...
written 5 months ago by Ashastry60
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Answer: A: RNA-seq: is there a way to get the variability between biological replicates ?
... Correlation matrix can answer your question. Although, I second the thought that it is always better to have 3 replicates for such analysis. DESEQ2 accounts for extreme variabilities in it's model if there are more replicates. They also recommend box plots to detect the outliers, Again,with more rep ...
written 5 months ago by Ashastry60
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Answer: A: DESeq2 contrasts - creating different objects or not?
... "should I create a separate DESeq object for each contrast using only the samples" Create one object. and then for comparison, do this - res, comparison1<-results(dds, contrast = c("A.untreated", "B.treated")) and so on. You can list the contrast names in the object by doing resultNames( ...
written 5 months ago by Ashastry60
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Comment: C: How to add biological annotations using R
... mart<-useMart(biomart ="ensemble", dataset = "") ...
written 5 months ago by Ashastry60
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Answer: A: Question in RNA-Seq gene expression profiling
... If they are saying they used 0.1 as the cutoff then they probably used that cutoff on the counts table and not the gtf file. There are several arguments about FPKM cutoff and you can look them up on biostars to understand it. If you want to have an overview of what is in your RNAseq data, I would r ...
written 6 months ago by Ashastry60
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Answer: A: How to add biological annotations using R
... BiomaRt is my first option. Although, I occasionally use AnnotationDBI package. ...
written 6 months ago by Ashastry60

Latest awards to Ashastry

Scholar 5 months ago, created an answer that has been accepted. For A: How to export heatmap clusters to csv?
Scholar 6 months ago, created an answer that has been accepted. For A: How to export heatmap clusters to csv?

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