User: capricygcapricyg

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Posts by capricygcapricyg

<prev • 18 results • page 1 of 2 • next >
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Comment: C: output of the function "makeCountsFromAbundance"
... Thank you very much! ...
written 19 days ago by capricygcapricyg0
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output of the function "makeCountsFromAbundance"
... Hello, there, I am testing the function "makeCountsFromAbundance" using the following data (numbers derived from Salmon output): ``` > count a b c d A 27 50 67 36 B 0 0 0 0 > length a b c d A 310.08 395.79 504.53 342.48 B 1026.00 1008.00 1009.00 1021.0 ...
tximport written 21 days ago by capricygcapricyg0 • updated 20 days ago by James W. MacDonald50k
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(Closed) output of the function "makeCountsFromAbundance"
... Hello, there, I am testing the function "makeCountsFromAbundance" using the following data (numbers derived from Salmon output): > count a b c d A 27 50 67 36 B 0 0 0 0 > length a b c d A 310.08 395.79 504.53 342.48 B 1026.00 1008.00 1009.00 1021.00 > ...
tximport written 21 days ago by capricygcapricyg0
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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 5 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 5 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 5 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 5 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 6 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 6 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 6 months ago by capricygcapricyg0 • updated 6 months ago by davide risso830

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