Elyas Mohammadi

4 Questions 9 Answers 0 Followers

Questions related from Elyas Mohammadi

What does scale.factor do exactly in LogNormalize function in R and why it is 10000 by default?

Hi, In LogNormalize function feature counts for each cell are divided by the total counts for that cell and multiplied by the scale.factor prior to log transformation. My question is what does...

27 July 2020 2,152 2 View

How to exclude the repetition of gene-gene correlation calculation in python?

I am trying to make a paired matrix of gene-gene correlation. Considering that I have a huge matrix (13000 genes and 900 samples) and for some reasons I don't want to decrease the number of my...

31 January 2020 8,772 3 View

What should I do when I have "#NAME?" in my Log Fold Change data to calculate Z-score? replace with zero or what?

I am trying to calculate the Z-score for several columns with Log fold change (LFC) data from RNA-seq expression values. But the mean for all columns, except one of them, is -inf and the standard...

21 December 2019 1,768 5 View

HTseq software issue during RNA-seq analysis?

Hi everyone. I am doing a RNA-seq project on tomato gene expression. I am trying to convert my bam files to txt files by HTseq. My command is as follow: htseq-count -f bam 31_36.bam...

30 July 2019 4,459 3 View