User: sally.badawi

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Posts by sally.badawi

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Comment: C: Htseq files import via tximport
... Cant I obtain gene level counts (I already have transcripts counts) from the htseq files I have? Or originally counts should be read as genes in the htseq algorithm. If yes, any proposed function to do this? SummarizetoGene function also require a tximport file. Thank you ...
written 9 months ago by sally.badawi0
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Comment: C: Htseq files import via tximport
... If I try another option: sampleFiles <- grep("S",list.files(dir),value=TRUE) > txi <- tximport(sampleFiles, type = "none", geneIdCol = "UCSC_ID", countsCol = "Counts") Error in tximport(sampleFiles, type = "none", geneIdCol = "UCSC_ID", countsCol = "Counts") : all(file.e ...
written 9 months ago by sally.badawi0 • updated 9 months ago by Martin Morgan ♦♦ 24k
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Htseq files import via tximport
... Good morning, Ive been trying to import htseq files into tximport to transform count reads from transcripts to gene level, All files exist in directory. I am facing this error: txi <- tximport(files, type = "none", geneIdCol = "UCSC_ID", countsCol = "Counts") reading in files with read_tsv 1 Er ...
tximport importer written 9 months ago by sally.badawi0 • updated 9 months ago by Michael Love26k
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Data filtering in DESeq2
... Hello again, Actually, we know that you havent recommended data filtration before running DESeq function, claiming that it only affects the speed of the function running. Interestingly, when setting a filtration strategy based on the percentage of samples having zero read counts in our data, we fo ...
deseq2 data filtering written 9 months ago by sally.badawi0 • updated 9 months ago by Michael Love26k
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Comment: C: LRT test followed by filtering based on LFC
... No, I know how to access all data, I want to sort after LRT test based on the LFC I want genes having absolute LFC > 0,5 but I cant use LFCthreshold in LRT test results. So how can I filter based on FC? Or you recommend that I dont do this filtering originally? ...
written 9 months ago by sally.badawi0
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LRT test followed by filtering based on LFC
... Good morning, I know that LFC threshold and altHypothesis are applied only in Wald tests. Is there any way to sort out gene based on LFC thresholding post LRT test? LRT result tables usually provide pvalue of the tested hyposthesis and LFC for the specified conditions only. Would it be statistical ...
deseq2 lrt lfc written 9 months ago by sally.badawi0 • updated 9 months ago by Michael Love26k
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Deseq2 paired analysis
... Hi everyone,  I have this paired experiment: control (16) and treated (17) groups, each was submitted to SD and HF diet.  1) I want to know the effect of SD in control samples? count matrix contains control samples only and  design = ~ subject.n + Diet where subject.n is the samples origin (patie ...
deseq2 paired samples interaction terms written 13 months ago by sally.badawi0 • updated 13 months ago by Michael Love26k
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Model matrix not full rank
... Hi all,  I would like to use DESeq2 to analyze a time series experiment of 6 time points each time point with 8 replicates. 3 time points are made in different time than the others, therefore they have a different batch. My aim is to detect the genes varying over time in response to the treatment ...
deseq2 batch effect model matrix not full rank written 17 months ago by sally.badawi0 • updated 17 months ago by Michael Love26k

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