User: xiaoaozqd

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xiaoaozqd0
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Posts by xiaoaozqd

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how to deal with the cufflinks files
... In "Importing transcript abundance datasets with tximport" only the type of Salmon,kallisto and RSEM, but no information about the cufflinks files. Is there any example? ...
tximport written 17 months ago by xiaoaozqd0 • updated 17 months ago by Michael Love20k
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Answer: A: why two different makeContrasts have the same results?
... Heartfelt thanks for your answer! I will extract log-fold changes from con_NS.32_NR.26 and combine them to the result of con_RS with correct order. At last I will get all of the LogFC combined by con_NS.32_NR.26 and con_RS, while the p-values/FDRs just from the result of con_RS. Then I will just an ...
written 2.5 years ago by xiaoaozqd0
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Comment: C: why two different makeContrasts have the same results?
... Thank you very much for your explain and sorry for the bad English! "except colume" is the result of the  fold change between goupingNS.32.xx and goupingNR.26.xx, you guess  is very accurate. My last question is about the FDR. Can I use both the FDR and p-values in the result of con_RS for con_NS. ...
written 2.5 years ago by xiaoaozqd0
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Comment: C: why two different makeContrasts have the same results?
... Thank you very much for your explain! You got it,"hpi" symbol as "hours post-infection" , "NR/NS" symbol as the different plant, "32/26" symbol as different fungi. You means in the "con_RS" the software had been contrasts between groupingNR.32.xx-groupingNS.32.xx, groupingNR.32.xx-groupingNR.26.x ...
written 2.5 years ago by xiaoaozqd0
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Comment: C: why two different makeContrasts have the same results?
... counts <- read.csv("All_Fragments.exp20160520.csv") plant = c(rep("NR",3),rep("NS",3),rep("NR",15),rep("NS",15),rep("NR",15)) fungi <- c(rep("MK",6),rep("32",30),rep("26",15)) time <- c(rep("0hpi",6),rep("18hpi",3),rep("24hpi",3),rep("48hpi",3),rep("96hpi",3),rep("168hpi",3),rep("18hpi", ...
written 2.5 years ago by xiaoaozqd0
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why two different makeContrasts have the same results?
... When I used the edgeR analyzed the DE genes, there are two different Contrasts: con_RS <- makeContrasts( (groupingNR.32.18hpi-groupingNR.MK.0hpi)-(groupingNR.26.18hpi-groupingNR.MK.0hpi), (groupingNR.32.18hpi-groupingNR.MK.0hpi)-(groupingNS.32.18hpi-groupingNS.MK.0hpi), (groupingNR.32.24hpi-grou ...
edger makecontrasts written 2.5 years ago by xiaoaozqd0
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Comment: C: how to use edgeR analysis RNA-seq data with a obvious deviation sample
... Thank you very much for your advice, you well explained my doubts. I’m so sorry about the confuse description. In the code I used NR instead of NILR, NS instead of NILS, MK.usp instead of 0h. In my MDS plot among the six time-points, only one or two points are clustering by batch. So I decide to ...
written 2.7 years ago by xiaoaozqd0
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Comment: C: how to use edgeR analysis RNA-seq data which has four factors
... thank you very much of your replay, the new post in https://support.bioconductor.org/p/80327/ ...
written 2.7 years ago by xiaoaozqd0
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how to use edgeR analysis RNA-seq data with a obvious deviation sample
... the raw code: ######################################################## > plant = c(rep("MK",5),rep("NR",30),rep("NS",15)) > fungi = c(rep("32",2),rep("26",18),rep("32",30)) > time = c(rep("usp",5),rep("18hpi",3),rep("24hpi",3),rep("48hpi",3),rep("96hpi",3),rep("168hpi",3),rep("18hpi",3), ...
edger anova rna-seq written 2.7 years ago by xiaoaozqd0 • updated 2.7 years ago by Aaron Lun21k
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Answer: A: how to use edgeR analysis RNA-seq data which has four factors
... Could you kindhearted to help me again?  In my data, one biological repeat (CYR32_1) in one group is obvious deviation from the other two biological repeats(CYR32_2 and CYR32_3) in the plotMDS with or without the method BCV. So I just removed this sample, while when the design (= model.matrix(~ 0 ...
written 2.7 years ago by xiaoaozqd0

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