User: Eugene A

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Eugene A0
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Posts by Eugene A

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Comment: C: Individual genes plots after batch correction with Deseq2
... something like this (given matrix with row - gnes, sample - columns): pritty_boxplot <- function(matrix, masker, row, deseq_res = FALSE){ #print nice boxplot for given row in dataframe (matrix) #masker - columns lables if(!deseq_res){ ...
written 5 hours ago by Eugene A0
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Comment: C: Differential expression with leave one out?
... Thanks! I'll keep it in mind next time. Although I'd say that 39 is a not that small number when have to be validated in the lab -> my task was to reduce the list of genes as far as possible. ...
written 11 months ago by Eugene A0
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Comment: C: Individual genes plots after batch correction with Deseq2
... Thanks for the answer!! Shame but it did not occur to me that vst is indeed that much close to the log transformation. Best, Eugene PS I'd mark your comment as an answer, if I could ...
written 11 months ago by Eugene A0
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Comment: C: Individual genes plots after batch correction with Deseq2
... Hi! I meant that after vsd transformation, genes with let say 1000 and 10 reads will be at the same scale. Nevertheless, the gene with 1000 reads was, probably, detected with higher accuracy, so I'd like to preserve such info. May be for this I should somehow switch to TPMs, but I'd like to avoid it ...
written 11 months ago by Eugene A0
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Individual genes plots after batch correction with Deseq2
... Hi everyone, I'm performing analysis of some RNAseq samples, and currently trying to cope with batch effect.plotting PCA of vsd transformed data, I can clearly see two batches which are differ fromt the others. plotPCA(vsd, intgroup = c('batch'),ntop= 34085) ![PCA][1] If I'm not mistaken, the ...
R deseq2 rna-seq written 11 months ago by Eugene A0
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Comment: C: troubles with exon coordinate extraction from ucsc
... Thanks! Probably I indeed will work around it. I just naively thought that getting the exon coordinates for set of genes from the ucsc should be one step procedure. ...
written 20 months ago by Eugene A0
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Comment: C: troubles with exon coordinate extraction from ucsc
... Thanks! I'm new to biostar so I did not know about that option. ...
written 20 months ago by Eugene A0
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troubles with exon coordinate extraction from ucsc
... May be this is some misunderstanding from my side but I failed to figure it out so far. I'm trying to extract exons coordinates for given set of genes (in bed format) from UCSC, which seems to be a straite forward task. here the one line example from the bed file (the coordinates are in hg38): ...
genome software error sequence written 20 months ago by Eugene A0 • updated 20 months ago by RamRS26k
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Differential expression with leave one out?
... Hi everyone, I have a general question concerning RNAseq analysis. I'm running the analysis, comparing 17 vs 39 biological replicas and the goal is to identify biomarkers for these two group. In order to identify DE genes I'm using DESeq2. I filter the resulting list by Log2fold change >1,<-1 ...
deseq2 rna-seq written 23 months ago by Eugene A0 • updated 11 months ago by Devon Ryan94k

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