User: bijaya.malla

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Posts by bijaya.malla

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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 3 months ago by bijaya.malla0
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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 3 months ago by bijaya.malla0 • updated 12 weeks ago by Michael Love16k
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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 4 months ago by bijaya.malla0
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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 4 months ago by bijaya.malla0
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DGEList error ?
... I imported a data as follows which has first column as genes name and other 21 columns for samples with respective counts for genes using >d=read.csv("path/xyz.csv", as.is=T) THEN, define group using c function >group=c("control", "test", "n") >library(edgeR) >dge=DGEList(d,group=gro ...
data import written 4 months ago by bijaya.malla0 • updated 4 months ago by James W. MacDonald45k
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RNA-seq workflow at the gene level - "colSums(assay(se))" command ?
... Can someone explain me where the numbers, especially the one after "colSums(assay(se))" comes from ? e.g. SRR1039513_subset.bam ## 6478 Thanks head(assay(se), 3) ## SRR1039508_subset.bam SRR1039509_subset.bam SRR1039512_subset.bam ## ENSG00000009724 38 ...
rnaseq summarized experiment written 13 months ago by bijaya.malla0 • updated 13 months ago by Michael Love16k

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