Question: Normalize miRNA expression matrix from reads count table
0
gravatar for landscape95
6 months ago by
landscape9580
landscape9580 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 • 293 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by landscape9580

Does anyone have a solution to this problem?

ADD REPLYlink written 4 months ago by DataKimist0

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 4 months ago • written 4 months ago by cpad01123.6k

Thanks for your reply. Both the workflow and datatype names had been changed in the package, so I needed to match those names. Works fine now.

ADD REPLYlink written 3 months ago by DataKimist0
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