User: ag1805x

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ag1805x90
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Posts by ag1805x

<prev • 106 results • page 1 of 11 • next >
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Comment: C: How filter genes to construct co-expression network?
... Is it good to use DESeq2 normalized count for WGCNA. The counts obtained by `counts(dds, normalized=TRUE)` ...
written 5 weeks ago by ag1805x90
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Comment: C: How to graphically tell if data has been normalized?
... I guess I need a bit more of help regarding this. I going through the graphs generated by the first three methods and something feels bad is going on; especially if you see box plot of normalized counts and density plot. Please see the attached files. The plots are similar for all of them so represe ...
written 7 weeks ago by ag1805x90
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Comment: C: How to graphically tell if data has been normalized?
... So what's your opinion on using this. Something else I should try. Apart from this if I read correctly DESeq performs further cleaning. ...
written 8 weeks ago by ag1805x90
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Comment: C: How to graphically tell if data has been normalized?
... I was experimenting with several like: 1) rowSums(count) > 0 2) rowMeans(count) > 1 3) rowSums(count>0)>10 4) apply(count, 1, function(x){all(x>0)}) The plots I provided above are from #4 and this is from DESeq2 manual (if I remember correctly). Initi ...
written 8 weeks ago by ag1805x90
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Answer: A: Finding orientation of single-ended reads (R or F)
... If you are looking for STRANDNESS then use infer_experiment.py from RseQC. Refer http://rseqc.sourceforge.net/ & https://chipster.csc.fi/manual/library-type-summary.html ...
written 8 weeks ago by ag1805x90
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Comment: C: removing outliers before running DESeq2
... Why 10? Why not any other? ...
written 8 weeks ago by ag1805x90
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Comment: C: How to graphically tell if data has been normalized?
... Thank you very much. This is really going to help me. I more thing I need to clear. For box/violin plots do the first/third quartile or median for all the samples be at the same levels. For the same data set i was trying a different low count filter and after that I saw that the third quartile and ...
written 8 weeks ago by ag1805x90
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Comment: C: error in getting results from DESeq2
... Any particular reason for choosing **10** and **300** in > rowSums((counts(dds)) >= 10) >=300 I have seen several papers/tutorials using different strategy like rowSums>0 to filter low count genes, but I could never get the real reason. ...
written 8 weeks ago by ag1805x90
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How to graphically tell if data has been normalized?
... Is there a method to tell if my RNA-seq data has been normalized? I used DESeq2 to normalize my feature count data and they plotted the log transformed normalized counts with box-plots. Is this a good way to analyse? I had referred some articles where they had used this method. For median normalizat ...
normalization deseq2 rna-seq written 9 weeks ago by ag1805x90 • updated 9 weeks ago by Kevin Blighe28k
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Comment: C: Number of Transcripts in GRCh38
... Just looking for a small cross verification. The number of transcripts is 199184; what is the number of genes in this build? Is it 60675? So after read assignment with FeatureCounts/Stringtie I expect to get count for 60675 genes? ...
written 12 weeks ago by ag1805x90

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