[BioC] The issue with Report Pearson instead of Spearman

[Wolfgang Huber]

Dear Ning

Try typing

  library("cellHTS2")
  ? getMeasureRepAgreement

into the R interpreter. You'll get:

Value:

      The function generates a list with elements:

      "repStDev": matrix with the calculated repeatability standard
      deviation between plate replicates. It has dimensions 'nrPlates x
      nrChannels';

      "corrCoef" (if the number of replicates equals 2): matrix with the
      correlation coefficients between plate replicates. It has
      dimensions: 'nrPlates x nrChannels';

      "corrCoef.min" (if the number of replicates is greater than 2):
      matrix with the minimum value of the correlation coefficients
      between plate replicates. It has dimensions 'nrPlates x
      nrChannels';

      "corrCoef.max" (if the number of replicates is greater than 2):
      matrix with the maximum value of the correlation coefficients
      between plate replicates. It has dimensions 'nrPlates x
      nrChannels'.

Does this answer your question?


	Best wishes
	Wolfgang


On 13/08/10 17:47, Ning wrote:
> Hi Wolfgang,
>
> Thank you for your help. Please forgive me always asking some naive questions as
> I have never used the R language before and I have to learn everything from zero.
>
> My question is how I can show the correlation with “pearson” instead of
> "spearman" in the HTML reports.
>
> My understanding is when I call
>
> repAgree<- getMeasureRepAgreement(xn, corr.method = "pearson"),
>
> the results are stored in the asssayData slot of the cellHTS2 object.
>
> Then how can I let it show in the reports?
>
> Thank you so much!
>
> Ning
>
> sessionInfo()
>
> cellHTS2
> R version 2.11.1(2010-05-31)
>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber