User: Fahmi Nazarie

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Posts by Fahmi Nazarie

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Answer: A: DEXSeq - Error in estimateSizeFactorsForMatrix(featureCounts(object)
... Just one question on computational time of DEXSeq. How long does it take to finish for estimateDispersions step? I set BPPARAM = MulticoreParam(workers=24). I wonder if it will take long time to finish the job. Does it take long time for DEU step too?  ...
written 4.2 years ago by Fahmi Nazarie0
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Answer: A: DEXSeq - Error in estimateSizeFactorsForMatrix(featureCounts(object)
... Gotcha! Thanks Wolgang and Michael. I resolved the issue. As you mention from the descriptive statistics at least one sample has all zeros, definitely something went wrong on count read file on that particular sample. I checked the BAM file that I used for read counting got problem. I will have re-r ...
written 4.2 years ago by Fahmi Nazarie0
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Answer: A: DEXSeq - Error in estimateSizeFactorsForMatrix(featureCounts(object)
... I don't think these samples have all zero maybe apart of it only. What is your recommendation for the estimation size factor here? Below are the descriptive summaries.   ​> dim(cts) [1] 579556 154 > summary(colSums(cts)) Min. 1st Qu. Median Mean 3rd Qu. Max. 0.000e+ ...
written 4.2 years ago by Fahmi Nazarie0
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DEXSeq - Error in estimateSizeFactorsForMatrix(featureCounts(object)
... Hello I do have a problem here. I am using DEXSeq to analyse exon usage across 27 different human tissues. Each tissues have 3 replicates and some of them have 2 replicates. The error came out when I want to EstimateSizeFactors: > dxd = estimateSizeFactors(dxd) Error in estimateSizeFactorsForM ...
dexseq deseq2 alternative splicing written 4.2 years ago by Fahmi Nazarie0
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Comment: C: DESeq2 - Error in estimateSizeFactorsForMatrix(counts(object)
... Alright, thanks Michael for your help. ...
written 4.2 years ago by Fahmi Nazarie0
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Comment: C: DESeq2 - Error in estimateSizeFactorsForMatrix(counts(object)
... What I do is like this as says in vignette res<- results(dds2, contrast=c("condition" , "Brain" , "Thyroid" )) But I have 27 different tissues, if I make results one by one it will take an ages to finish. How can I extract all these in one command and place it in one file of 'res'?   ...
written 4.2 years ago by Fahmi Nazarie0
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Answer: A: DESeq2 - Error in estimateSizeFactorsForMatrix(counts(object)
... Hi Michael I solved the problem. How do I get list of all genes (row) vs tissues (27 different tissues - column) with all the p-value or p-adjsuted value. I just could not find the command line in any questions or manual. Thanks ...
written 4.2 years ago by Fahmi Nazarie0
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Answer: A: DESeq2 - Error in estimateSizeFactorsForMatrix(counts(object)
... The error occured when I ran this code, which after I filtered out '0' value in my dataset. dds = estimateSizeFactors(dds, geoMeans=geoMeans)   I am not sure if there is a package called trackback(). > trackback() Error: could not find function "trackback"   Here is the summary for geoMe ...
written 4.2 years ago by Fahmi Nazarie0
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Answer: A: DESeq2 - Error in estimateSizeFactorsForMatrix(counts(object)
... Thank Michael for replying my message. I have followed your advice, but I have got an error. I removed all the gene with 0 value by using  dds = ddsHTSeq[ rowSums(counts(ddsHTSeq)) > 5, ] Then    cts = counts(dds)  geoMeans = apply(cts, 1, function(row) if (all(row == 0)) 0 else exp(mean(log ...
written 4.2 years ago by Fahmi Nazarie0
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DESeq2 - Error in estimateSizeFactorsForMatrix(counts(object)
... Dear Michael Love I got a problem running DESeq2. Briefly, I have 27 different human tissue and each of them has 3 replicates and some of them only has 2 replicates with a total 76 samples. I want to study the differential expression across the human tissue. I wanna get which gene has differential ...
deseq2 written 4.2 years ago by Fahmi Nazarie0

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