## User: Mike

Mike10
Reputation:
10
Status:
New User
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Last seen:
6 months, 1 week ago
Joined:
1 year, 11 months ago
Email:
m*****@uwo.ca

#### Posts by Mike

<prev • 14 results • page 1 of 2 • next >
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... results1 <- results( dds, contrast=c("combined","B_treated","B_untreated") ) results2 <- results( dds, contrast=c("combined","B_treated","B_untreated"), lfcThreshold=0.58496 ) summary(results1) summary(results2) Output. The results are different but they both say "LFC > 0 (up)" and "LFC ...
written 8 months ago by Mike10 • updated 8 months ago by Michael Love20k
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... I have 4 RNA-seq samples A,B,C,D in triplicate. They're aligned with STAR and counted with summarizeOverlaps, following the Bioconductor RNA-seq workflow. I'm comparing A vs B and C vs D (other comparisons later but these for now). I'm getting different and odd patterns in the MA-plot depending on w ...
written 8 months ago by Mike10 • updated 8 months ago by Ryan C. Thompson7.0k
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... I checked the distribution of pvalues and the results for 'contrast' don't look right. hist(results.A$pvalue[results.A$baseMean > 1], breaks = 0:20/20, col = "grey50", border = "white") hist(results.B$pvalue[results.B$baseMean > 1], breaks = 0:20/20, col = "grey50", border = "white") hist(re ...
written 10 months ago by Mike10
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... Thanks I used the modified command and it worked. I get very few genes changed in the contrast which may be correct (PCA shows the samples are similar) but just want to ensure I'm doing this right: I first had to relevel treatment: se$treatment <- relevel(se$treatment, "untreated") Then analy ...
written 10 months ago by Mike10
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... Thank you for the reply. When I use design of ~celltype:treatment dds <- DESeqDataSet(se, design = ~cell_type:treatment) I get a matrix is not full rank error. I looked at the "Model matrix not full rank" in the vignette, should I follow the instructions under "Group-specific condition effects ...
written 10 months ago by Mike10
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... I have cell type A (untreated vs treated) and cell type B (untreated vs treated), 3 replicates for each: sample cell_type treatment combined 1 A untreated A_untreated 2 A untreated A_untreated 3 A untreated A_untreated ...
written 10 months ago by Mike10 • updated 10 months ago by Michael Love20k
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... One control and two treatments, I think that's the same situation as in this post: https://support.bioconductor.org/p/104783/ ...
written 10 months ago by Mike10
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... 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 13 months ago by Mike10
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... 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 ...
written 13 months ago by Mike10 • updated 13 months ago by Ryan C. Thompson7.0k
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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 14 months ago by Mike10

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