User: capricygcapricyg

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Posts by capricygcapricyg

<prev • 21 results • page 1 of 3 • next >
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Comment: C: cross-array comparison using limma fitted values
... Thank you very much for your reply! We have done meta-analysis as you mentioned. But, we are still interested in comparing mouse and human at condition A since we actually would like to know if mouse is reasonable model for human... Regarding the batch effect, may I do "normalizedBetweenArrays" us ...
written 5 weeks ago by capricygcapricyg0
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cross-array comparison using limma fitted values
... Hello there, My mouse array data and human array data were derived from the same two conditions, condition A and condition B. I fitted two array data individually using limma and the fitted expression values were obtained using the as.matrix(y). Now my question is: may I directly compare the mouse ...
limma written 5 weeks ago by capricygcapricyg0 • updated 5 weeks ago by Aaron Lun24k
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Number of profiles in JASPAR2018
... Hello, there, I would like to get all the mouse transcription factors from Jasper using this package and some how found it only has 119 records. ``` > library(JASPAR2018) > opts=list(species=10090) > library(TFBSTools) > jaspar_data=getMatrixSet(JASPAR2018,opts) > length(jaspar_data ...
jaspar2018 written 6 weeks ago by capricygcapricyg0
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Comment: C: output of the function "makeCountsFromAbundance"
... Thank you very much! ...
written 11 weeks 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 11 weeks ago by capricygcapricyg0 • updated 11 weeks 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 11 weeks 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 7 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 7 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 7 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 7 months ago by capricygcapricyg0

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