User: capricygcapricyg

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Posts by capricygcapricyg

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Comment: C: salmon output for DESeq2 analysis
... Hi, James, As you mentioned that we don't know what the base truth is, whenever the outputs are different, I just would like to know if anyone has ever tested which one makes more sense... C. ...
written 3 months ago by capricygcapricyg0
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Comment: C: salmon output for DESeq2 analysis
... I have different concerns, actually: counts data usually come from genome alignment; however, salmon data from the transcriptome alignment. I found tximport converted counts were not really matching the genome alightment-based counts... ...
written 3 months ago by capricygcapricyg0
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Comment: C: salmon output for DESeq2 analysis
...   Michael, Thank you very much for your quick response! To make sure my understanding is correct, I found the following paper: https://www.ncbi.nlm.nih.gov/pubmed/26925227 And you conclusion is: "salmon->tximport->DESeq2" is better than "counts->DESeq2"? Kind regards, C. ...
written 3 months ago by capricygcapricyg0
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salmon output for DESeq2 analysis
... HI, Michael, I read your DESeq2 vignette: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html and found that DESeqDataSet could be derived from the salmon output (Transcript abudance) or count matrix. I wonder if you ever compare the results of these two process (sal ...
deseq2 written 3 months ago by capricygcapricyg0
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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 4 months 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 4 months 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 4 months ago by capricygcapricyg0 • updated 4 months ago by davide risso810
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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 4 months 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 4 months ago by capricygcapricyg0 • updated 4 months ago by davide risso810
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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 5 months ago by capricygcapricyg0

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