User: Mike

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Mike10
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Posts by Mike

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Will large differences in the number of reads between samples decrease reliabili
... Thanks that's good to know. >This looks like a reasonable, expected variation in total read counts. We sequenced on a NextSeq and expected the reads evenly distributed between the 8 samples and I was surprised by the variability, I expected some but not this much. I was planning to follow up wi ...
written 20 days ago by Mike10
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Will large differences in the number of reads between samples decrease reliability of DESeq2 analysis?
... I have some RNA-seq samples from mouse, 2 conditions with 4 replicates each, read quality is good and for each sample 85-90% of reads align. The number of aligned reads in millions are: Condition 1 replicate 1: 100 Condition 1 replicate 2: 79 Condition 1 replicate 3: 52 Condition 1 replicate 4: 37 ...
deseq2 written 20 days ago by Mike10 • updated 20 days ago by Ryan C. Thompson6.1k
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Comment: C: DESeq2 experimental design
... Thank you for your reply, I have some additional questions about the design formula. These are my 12 samples and let's assume I'm analyzing them all together: Sex Genotype BioRep Group female control 1 female.control female control 2 ...
written 5 weeks ago by Mike10
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DESeq2 experimental design
... I have 12 RNA-seq samples: 3 replicates each of male control, male mutant, female control, and female mutant. I want a list of genes that are significantly differentially expressed in male (mutant vs control) and female (mutant vs control). I'm not interested in comparing for example male control vs ...
deseq2 multiple factor design written 6 weeks ago by Mike10 • updated 6 weeks ago by Gavin Kelly510
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[DESeq2] Slight difference between lfcMLE and my calculated log2 fold change
... The values I calculate manually for log2 fold change (using R or Excel) are always slightly different than the lfcMLE value, I'm curious why that would be (sorry, stats isn't my strong suit). For example (each condition has 3 replicates): Condition 1 normalized counts: 18536.58274, 20600.98049, 225 ...
deseq2 written 8 weeks ago by Mike10 • updated 8 weeks ago by Michael Love14k
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Comment: C: Annotating DEseq output using AnnotationDbi mapIds and most results say NA
... Thank you it's working much better now but still missing about 10% of them. Actually it's matching everything up to ENSMUST00000195885 and getting NA for all subsequent transcript IDs, here are the 10 around ENSMUST00000195885: ENSMUST00000195877 RP24-144H23.5 ENSMUST0000019587 ...
written 10 months ago by Mike10
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Annotating DEseq output using AnnotationDbi mapIds and most results say NA
... I have a list of ~31,000 mouse transcripts with their Ensembl transcript IDs that I'm trying to annotate using AnnotationDbi and the org.Mm.eg.db database. R v3.3.2, the object containing the IDs is called "temp". My command is: mapIds(org.Mm.eg.db, keys=row.names(temp), keytype="ENSEMBLTRANS", co ...
annotationdbi org.mm.eg.db mapids ensembltrans written 10 months ago by Mike10 • updated 10 months ago by James W. MacDonald45k

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