Question: Normalize miRNA expression matrix from reads count table
0
gravatar for landscape95
3 months ago by
landscape9570
landscape9570 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

enter image description here

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 [2] must be the same length as the vector [0]
Timing stopped at: 0.004 0 0.003

I think of 2 problems here:

  1. I dont have the right "geneInfo" -> how can I get the right one?
  2. 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!

mirna • 169 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by landscape9570

Does anyone have a solution to this problem?

ADD REPLYlink written 8 days ago by kimist990

for gene info: https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/19. Look at the last comment. Once you have that you may need to match the miRNA list between your df and geneinfo.

ADD REPLYlink modified 8 days ago • written 8 days ago by cpad01121.7k
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