User: ag1805x

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ag1805x10
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http://ag1805x.github.io/
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1 month, 1 week ago
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9 months ago
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Posts by ag1805x

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Comment: C: DESeq2 FPKM normalization
... So if we need to compare between two sets of data from two different experiments, is it worth using COMBAT to remove batch effect and then use edgeR to normalize by TPM and DE analysis? ...
written 9 weeks ago by ag1805x10
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Comment: C: log2FoldChange calculation in DESeq2 output
... When calculating fold change how is the reference group determined? ...
written 4 months ago by ag1805x10
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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 4 months ago by ag1805x10
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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 months ago by ag1805x10 • updated 5 months 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 months ago by ag1805x10
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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 months ago by ag1805x10
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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 8 months ago by ag1805x10
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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 9 months ago by ag1805x10
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Comment: C: How fold change is calculated in Ballgown?
... Is KO & WT the covariate considered during stattest?  ...
written 9 months ago by ag1805x10
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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 9 months ago by ag1805x10 • updated 9 months ago by James W. MacDonald48k

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