User: ag1805x

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ag1805x0
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Posts by ag1805x

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Comment: C: log2FoldChange calculation in DESeq2 output
... When calculating fold change how is the reference group determined? ...
written 22 days ago by ag1805x0
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Comment: C: "Over-correction" in the size-factors of the DESeq2 package
... What is a good range for size factors? In the manual I saw it should be near to 1. How much can it vary?  ...
written 24 days ago by ag1805x0
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What are the different strategies to filter out low count genes?
... What are the different strategies to filter low count genes? Some of the ones I have seen in different papers are: rowSums(count)>0 rowVariance(count)>1 ...
rnaseq deseq2 differential gene expression written 5 weeks ago by ag1805x0 • updated 4 weeks ago by Wolfgang Huber13k
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Comment: C: Too many (?) differentially expressed genes - edgeR and DESeq
... Hi Darya, I am working with something similar. Even I found about 49% of the ~20k protein Coding genes to be deferentially expressed. If you could share how you dealt with this or justified the observation. ...
written 5 weeks ago by ag1805x0
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Comment: C: DESeq2 vs Ballgown results
... Same problem with my data. Huge difference between DEG reported by Ballgown and DESeq2. I have now shifted from Hisat2>Stringtie>Ballgown to using Hisat2>FeatureCounts>DESeq2. Is this combination good? ...
written 5 weeks ago by ag1805x0
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Comment: C: Ballgown up and down regulated genes
... How many replicated do you have per group? I had similar problem when I had 2 replicates per group; but increasing it to 3 solved the problem.  ...
written 4 months ago by ag1805x0
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Comment: C: How fold change is calculated in Ballgown?
... Is any log transformation done on the FPKM values during FC calculation? I tried to manually calculate the FC by extracting the FPKM values for few genes using gexpr(), but the result I obtained differs considerably from the stattest result. Also after stattest the genes that were supposed to be up ...
written 5 months ago by ag1805x0
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Comment: C: How fold change is calculated in Ballgown?
... Is KO & WT the covariate considered during stattest?  ...
written 5 months ago by ag1805x0
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What is the exact formula for the calculation of Fold Change (FC), p-val and q-val in Ballgown stattest?
... I am looking for the exact formula for the calculation of Fold Change (FC), p-val and q-val in Ballgown stattest? By using gexpr I got the gene expression values for the list of genes. For better understanding I tried to calculate the FC for a few genes manually but the values I obtained differed f ...
ballgown fold change stattest written 5 months ago by ag1805x0 • updated 5 months ago by James W. MacDonald47k

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