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 5 days ago by Björn0 • updated 5 days 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 21 days ago by Björn0 • updated 21 days ago by Michael Love18k
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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 8 weeks 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 8 weeks 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 9 weeks ago by Björn0 • updated 9 weeks ago by Michael Love18k
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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 3 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 7 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 7 months ago by Björn0 • updated 7 months ago by Michael Love18k
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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 8 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 8 months ago by Björn0

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For DGEList error ?

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