Question: Normalize miRNA expression matrix from reads count table
5 months ago by
landscape95 • 70
landscape95 • 70 wrote:
Hi everyone, I have an miRNA expression matrix (in the picture below), when I try to normalize the data with
TCGAanalyze_Normalization(miRNA_data, geneInfo) I have some troubles
I Need about 0 seconds for this Complete Normalization Upper Quantile [Processing 80k elements /s] Step 1 of 4: newSeqExpressionSet ... Step 2 of 4: withinLaneNormalization ... Error in names(y) <- 1:length(y) : 'names' attribute  must be the same length as the vector  Timing stopped at: 0.004 0 0.003
I think of 2 problems here:
- I dont have the right "geneInfo" -> how can I get the right one?
- There seems to be the rows (which stands for genes) which seems like they are in the family of Accession numbers as I search on http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000062. Eg. "MIMAT0000062" owns Stem-Loops "hsa-let-7a-1, hsa-let-7a-2, hsa-let-7a-3". I want to normalize data that rows for accession numbers and columns for samples. How can I solve this?
Your help is really appreciated!
ADD COMMENT • link •