User: Yuqia

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Yuqia0
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Posts by Yuqia

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Comment: C: Error in designAndArgChecker(object, betaPrior) : variables in the design for
... I figured it out. It's a typo mistake in 1 sample name in the Design file. Thank you very much again Michael! and sorry for the false alarm! ...
written 13 months ago by Yuqia0
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Comment: C: Error in designAndArgChecker(object, betaPrior) : variables in the design for
... > any( is.na( dds$treatment ) ) [1] TRUE This is my Design file: Sample_ID    treatment    replicate sample1    A    R1 sample2    B    R1 sample3    A    R2 sample4    B    R2   ...
written 13 months ago by Yuqia0
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Comment: C: Error in designAndArgChecker(object, betaPrior) : variables in the design for
... Hi Michael, Thanks a lot for your very quick reply. I have this error for running your suggested function: > anyis.na(dds$treatment) Error in anyis.na(dds$treatment) : could not find function "anyis.na" ...
written 13 months ago by Yuqia0
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Error in designAndArgChecker(object, betaPrior) : variables in the design formula cannot have NA values
... Hi everyone, I used DESeq2 for DE analysis of featureCounts data from RNAseq of 2 treatments (A & B) with 2 replicates each. I have the same error as in this thread: https://support.bioconductor.org/p/85500/ Error in designAndArgChecker(object, betaPrior) :   variables in the design formula c ...
deseq2 featurecounts error message written 13 months ago by Yuqia0 • updated 13 months ago by Michael Love25k
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Answer: A: incorrect biomaRt output order of gene list
... Hi James, Thank you very much! That sounds great! I'll try that. Hi cherlyn, the V1 is the automatic header of the list when I use as.vector(list). But when I use read.csv to import the data, the list does not have that V1. Thank you for your input. I'll try that as well. ...
written 19 months ago by Yuqia0
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incorrect biomaRt output order of gene list
... Hello, I have another problem with biomaRt. My ranked list of differentially expressed genes (ENSG...) are not ordered by the id number but by the expression fold change (naturally): > library(biomaRt) > mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl") > list &l ...
biomart error ensembldb written 19 months ago by Yuqia0
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Answer: A: converting ensembl transcript ID to ensemble gene: problem & missing values
... Hello again, I have another problem with biomaRt. My ranked list of differentially expressed genes (ENSG...) are not ordered by the number but by the expression fold change (naturally): > library(biomaRt) > mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl") > list ...
written 19 months ago by Yuqia0
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Answer: A: converting ensembl transcript ID to ensemble gene: problem & missing values
... Awesome! Your code works perfectly. Thanks a lot Mike! ...
written 19 months ago by Yuqia0
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converting ensembl transcript ID to ensemble gene: problem & missing values
... Hello,   I have a long list of splice variants (ENSTxxx.y) from a DESeq2 experiment that I want to convert to the "clone_based_ensembl_transcript" and "clone_based_ensembl_gene" list. I used biomaRt v2.34.2 to test 3 transcripts in the list to make sure it works before converting the entire list: ...
biomart error ensembldb written 19 months ago by Yuqia0

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Popular Question 13 months ago, created a question with more than 1,000 views. For converting ensembl transcript ID to ensemble gene: problem & missing values

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