User: soheilazareie

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Posts by soheilazareie

<prev • 6 results • page 1 of 1 • next >
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Comment: C: DESeq2 use of LRT
... Hi Michael, Thanks for the reply, I would appreciate your help. our question is that considering 3 factors other than condition (3 levels, A, A1, D) which includes sex, passage of cells and different batches of expermint, what are the differntially expressed genes across all our samples (35, 14 D, ...
written 16 months ago by soheilazareie0
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DESeq2 use of LRT
... Hi I have a question regarding RNAseq data analyses by DESeq2, I have some data with 3 conditions (A, A1, D) and 3 other factors (P, B, Sex) with 2 or 3 levels in each, my question is that if I use LRT without any contrast, is that correct to imply whatever results give me as a final output for c ...
deseq2 written 16 months ago by soheilazareie0 • updated 16 months ago by Michael Love26k
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Comment: C: BAM file into R from Illumina
... thanks, but how it will detect the URL (I mean the exact path), in this code? ...
written 19 months ago by soheilazareie0
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BAM file into R from Illumina
... I have 49 bam files aligned by STAR through Illumina and just wondering if there is any way to export BAM files from illumina without downloading, for example into R, if someone helps me to understand how to load my files into a single read table through summarizeOverlaps I would really appreciate. ...
illumina star bam file written 19 months ago by soheilazareie0 • updated 19 months ago by ta_awwad10
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Comment: C: colData and design problem
... Thanks for the reply. here is one of the errors, Error in `rownames<-`(`*tmp*`, value = colnames(countData)) :    attempt to set 'rownames' on an object with no dimensions However, it looks like the above code now is working, but the other problem that I have had is this code: plotMA (DGE.res ...
written 20 months ago by soheilazareie0
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colData and design problem
... Hello, I would really appreciate if someone helps me understand my code better, I need help with writing design formulas/matrix is my coldata correct?...  I have 35 samples. Two different type of cell lines (which 2 or 3 of them have technical replicates as well) + control.  ac=15, dc=16, contr ...
deseq2 written 20 months ago by soheilazareie0

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