User: Björn

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Björn0
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Posts by Björn

<prev • 12 results • page 1 of 2 • next >
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Whether "read_counts_miRNA" or "reads_per_million_miRNA" to use for DE expression analysis using DeSeq2
... Hi, I downloaded HARMONIZED miRNA data from TCGA. The dataframe have two columns 1)reads_per_million_miRNA_mapped_TCGA-HC-7211-01A-11R-2117-13 and 2) raw_count_miRNAs. My questions 1. Should I use reads_per_million or raw_counts to compare DE miRNAs ? 2. I believe the "reads_per_million_miRNA" is ...
mirna normalization deseq2 tcgadownload written 4 months ago by Björn0 • updated 4 months ago by Lorena Pantano90
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How to find non-DE miRNAs using Deseq2 ?
... Hi, as most of the RNA sequencing analysis is focused on identifying DE miRNA expressed between comparison groups. How about non-DE miRNA is prospective study.  Scenario 1. Suppose, I am investigating impact of Drug A for Cancer treatment. My hypothesis is that the expression of certain miRNAs shoul ...
deseq2 mirna target prediction mirna-seq differentially expression written 4 months ago by Björn0 • updated 4 months ago by Michael Love19k
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Comment: C: how to create csv file with name of gene from unique ID of lcpm ?
... I did it as you have said which I have in my first post.  ...
written 6 months ago by Björn0
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Comment: C: how to create csv file with name of gene from unique ID of lcpm ?
... Sorry, still can't find the solution ...
written 6 months ago by Björn0
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how to create csv file with name of gene from unique ID of lcpm ?
... after converting raw counts to cpm from data file using command lcpm<-cpm(y, log=T) head(lcpm) gives first row with unique numeric ID which denotes gene names from data file. How to export name of genes into *.csv file but with name of genes ? write.csv(highly_variable_lcpm, row.names=y2$gen ...
edger bioconductor lcpm written 6 months ago by Björn0 • updated 6 months ago by Michael Love19k
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Comment: C: LogFC: how do you determine the cutoff for differentially expressed genes?
... Hi just incase there are no DG genes identified. How to proceed ? Is it always necessary to get DE genes? Would be happy to get some resources to share data where it is possible to show that "there are no DE genes" . The findings could be "biologically" significant although statistically "not signif ...
written 7 months ago by Björn0
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Answer: A: Choosing a threshold for minimum counts in RNAseq
... Hi Ryan, your website is really informative. However, it is not clear how to choose CPM value  ...
written 11 months ago by Björn0
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Error in checkFullRank(modelMatrix) : the model matrix is not full rank, ?
... I used following command to filter out 3 groups (NC, BF, CF) out of 5 groups while remaining two groups are "AF" and "DF". design_NCaF <- filter(design, Groups1!="NC",Groups1!="BF",Groups1!="CF") However, at following command NCaF <- DESeqDataSetFromMatrix(data_max_woNCaF, colData=design_NC ...
genefilter deseq2 filter written 11 months ago by Björn0 • updated 11 months ago by Michael Love19k
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Comment: C: DGEList error ?
... Definitely, in this era, everyone google or try to find answer oneself. I did check the data by different ways I saved the file as tab delimited format (txt) and run command > sapply(file.txt, class)         X    B2_015    B2_016    B2_017   B2F_015   B2F_016   B2F_017    B3_003  "factor" "inte ...
written 12 months ago by Björn0
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Comment: C: DGEList error ?
... It is better to provide answer rather than just to comment. Now I am getting another error "Error in colSums(counts): "x" must be numeric" @James W. MacDonald   ...
written 12 months ago by Björn0

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Popular Question 5 months ago, created a question with more than 1,000 views. For DGEList error ?

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