User: b.nota

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b.nota290
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Posts by b.nota

<prev • 117 results • page 1 of 12 • next >
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Comment: C: edgeR design between and within subjects
... Thanks for your explanation. So for the last part, which is only possible as indirect comparison (MUT.TEM vs WT.TEM). What will be the meaning of the fold changes in the topTags results? So I understand that the patient blocking does not make sense for such comparison (since WT patient 1 is not the ...
written 3 months ago by b.nota290
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edgeR design between and within subjects
... Hello, I am trying to do edgeR analysis, such as described in 3.5 of the manual. My experiment is very alike, but I don't exactly understand how to get all the contrasts of my interests. Here some code: > data.frame(Genotype, Cell, Patient) Genotype Cell Patient 1 WT TCM 1 2 ...
edger design and contrast matrix written 3 months ago by b.nota290 • updated 3 months ago by Aaron Lun17k
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Comment: C: converting fasta file into bam file
... Hi nosheenfaiz09, You miss an essential step in your analysis: alignment. Usually reads (in fastq format) are aligned to a reference genome, the results from such an alignment are saved in bam format, which contains information about the reads and their genome-aligned coordinates. Without alignment ...
written 4 months ago by b.nota290
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Answer: A: Getting Differentially Expressed Genes from GOSeq Categories
... In the manual they give an example with stack and getgo function. In your case something like this should work: allGos <- stack(getgo(diff_exp_ensembl, 'mm10', 'ensGene', fetch.cats = 'GO:BP')) head(allGos) edit: "diff_exp_ensembl" should be the list of DE ensembl gene names To get only the ...
written 4 months ago by b.nota290
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Reactome_gene IDs are pathway IDs in biomaRt
... Hello, I've been trying to use biomaRt to get reactome IDs (from pathways) of given reactome_gene IDs, however I found out that the reactome_gene IDs ARE the pathway IDs. It is now not possible to get the matching pathways by these gene IDs.   For example library(biomaRt) ensembl = useMart("en ...
biomart written 4 months ago by b.nota290
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Comment: C: featureCount and bam
... Remember that you are working in R with Rsubread, the command line you use now in for bash/linux. What you need is your bam files, and an annotation file in gtf format. The threads are the number of processors in your computer system, if you have more than one you can define them here. If you use a ...
written 4 months ago by b.nota290
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Comment: C: featureCount and bam
... Did you find the manual? It's all in there.   ...
written 4 months ago by b.nota290
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Comment: C: Nonspecific filtering of microarray data
... I don't think you'll need nonspecific filtering. I think you're better of using limma, it looks like a multi-factorial (two-way anova) design. Examples are in limma's user's guide for these kind of designs. ...
written 5 months ago by b.nota290
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Comment: C: Nonspecific filtering of microarray data
... It depends on what kind of analysis it is you're doing. ...
written 5 months ago by b.nota290
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Answer: A: error in installing bioconductor
... Did you try http instead of https? ...
written 8 months ago by b.nota290

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Scholar 8 months ago, created an answer that has been accepted. For A: warning in R
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Supporter 19 months ago, voted at least 25 times.
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: warning in R
Scholar 19 months ago, created an answer that has been accepted. For A: warning in R
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Scholar 2.4 years ago, created an answer that has been accepted. For A: warning in R

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