User: capricygcapricyg

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Posts by capricygcapricyg

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Comment: C: normalized counts from RUVg run: is further library size normalization needed?
... I did see that running "betweenLaneNormalization()" makes difference in terms of the output of the normCounts(). So, I guess my questions are: is "betweenLaneNormalization()" required for the RUVg normalization? Does "RUVg()" alone take care of the library size-wise normalization?  I ask this quest ...
written 12 days ago by capricygcapricyg0
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Comment: C: normalized counts from RUVg run: is further library size normalization needed?
... Hi, Davide, Thank you very much for the response! Could you please clarify more about "first step"? Here are what I ran:  == require(RUVSeq) set.RUV=newSeqExpressionSet(as.matrix(counts.filtered),phenoData=data.frame(sampleInfo$condition,row.names=colnames(counts.filtered))) set1.RUV=RUVg(set ...
written 12 days ago by capricygcapricyg0
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normalized counts from RUVg run: is further library size normalization needed?
... Hi, RUVSeq support, After running RUVg, I got the normalized counts. My question is: are those counts also normalized against the library size? Thanks. Kind regards, C.         ...
ruvseq written 13 days ago by capricygcapricyg0 • updated 12 days ago by davide risso780
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Comment: C: determine k during RUVSeq
... Thank you for the quick response! I saw an general increase in within sample dispersion on PCA plot with increased k. Also, when k=1, the within sample dispersion increases when compared with non-corrected sample. Is it normal? Thanks a lot! C. ...
written 13 days ago by capricygcapricyg0
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determine k during RUVSeq
... Dear Support Team, I have RNA-seq data from 50 samples. I would like to run RUVSeq to correct the unwanted variables. I wonder if there is a general guide about how to choose k number during RUVg? The online documentation used 1, but I saw some discussion about using other numbers... Thanks a lot! ...
ruvseq written 16 days ago by capricygcapricyg0 • updated 15 days ago by davide risso780
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Comment: C: SVAseq and DESeq2 workflow
... Thank you very much, Michael! I will try these packages and see how the results look like... ...
written 4 weeks ago by capricygcapricyg0
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Comment: C: SVAseq and DESeq2 workflow
... I wonder what you would go with such type of data? ...
written 4 weeks ago by capricygcapricyg0
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Comment: C: SVAseq and DESeq2 workflow
... My issue here is that, unlike your example, the two batches contains completely different samples. I can't use the annotated  batch in the DESeq2 design matrix. So I went to follow your section 8, to take the "sequencing year"   as some hidden and unwanted effects. Since there are many SVs, I just w ...
written 4 weeks ago by capricygcapricyg0
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Comment: C: SVAseq and DESeq2 workflow
... Hi, Michael, I actually have a question about your workflow: you plotted SV values versus cell line (stripchart(svseq$sv[, i] ~ dds$cell, vertical = TRUE, main = paste0("SV", i))). So what do you expect from these figurse? How do you evaluate if the cell line effects are correctly adjusted? Some ...
written 4 weeks ago by capricygcapricyg0
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Comment: C: SVAseq and DESeq2 workflow
...   HI, Michael, Thank you very much for the response! Sounds like you don't feel it is too high? I saw your example with 8 samples from 4 cell lines and 2 dex conditions, but only specified 2 SVc. I have 3 conditions, A, B and C, but SVAseq calculated 9 SVs. So I am very concerned. Also I read some ...
written 4 weeks ago by capricygcapricyg0

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