User: b.nota

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b.nota2.7k
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Posts by b.nota

<prev • 434 results • page 1 of 44 • next >
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Comment: C: How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
... If you want an answer from the authors themselves, you should ask this question on the bioconductor support site. Usually Gordon Smyth replies within a day. https://support.bioconductor.org/t/Latest/ ...
written 6 hours ago by b.nota2.7k
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Comment: C: normalization of microarray data
... Use only arrays together that were all done on the same platform. ...
written 7 hours ago by b.nota2.7k
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Comment: C: normalization of microarray data
... A quick look at your GEO sets, tells me that both sets did not use the exact same platform. Might that be the problem? ...
written 7 hours ago by b.nota2.7k
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Comment: C: When is HTSeq Count Script used?
... I am not sure, I found it easier in usage... ...
written 8 hours ago by b.nota2.7k
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Answer: C: When is HTSeq Count Script used?
... HTSeq can be used for any DE tool that uses raw read counts (hence limma trend, edgeR, DESeq2). You can also try featureCounts instead of HTSeq, which I personally prefer. ...
written 8 hours ago by b.nota2.7k
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Comment: C: Best Program to use for DE Analysis
... Most people here would advice to use DESeq2, or similar tools such as limma trend/voom or edgeR. You'll have to get raw read counts first from your bam files, I prefer using featureCounts for this. ...
written 8 hours ago by b.nota2.7k
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Comment: C: multivariate analysis of RNA-seq
... You can use edgeR, DESeq, etc. for 2 way (or more way) analysis (factorial analysis). You'll have to define your linear model correctly. They have some examples in the user's guides. ...
written 1 day ago by b.nota2.7k
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Comment: C: How to do differential expression?
... I would advice not to do this, but use raw count data instead and go for limma or edgeR analysis. ...
written 2 days ago by b.nota2.7k
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Comment: C: How to cluster differential expressed genes from RNA-seq analysis?
... Do you mean you want the clusters that are formed after clustering? Check previous post about this, you'll need cutree command for that. https://www.biostars.org/p/86563/ ...
written 2 days ago by b.nota2.7k
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Comment: C: how to cut the gz. file by chromosome
... gz file means that it is gunzipped, similar as zip file on windows. It is compressed to save diskspace, and has nothing to do with real bioinformatics. use gzip command to make gz files of your vcf file. gzip your.vcf ...
written 2 days ago by b.nota2.7k

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Scholar 3 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
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