LiNk-NY
commented
4 years ago Hi @cdy371761145
The maintainer of this package has transferred maintainership to me and I am deprecating the function in question due to difficulty in maintaining said functions. If you or someone you know would like to maintain the functions listed in the NEWS.md file. Please create another package that depends on this one.
Best,
Marcel
Dear mksamur/RTCGAToolbox: hi~ When I use the "getDiffExpressedGene" function to test the RTCGAToolbox ,like
diffGeneExprs <- getDiffExpressedGenes(dataObject=brcaData,DrawPlots=TRUE, adj.method="BH", adj.pval=0.05, raw.pval=0.05, logFC=2, hmTopUpN=100, hmTopDownN=100)I found the heatmap did not show all genes ，did not like the sample be given.
So I check the code ,find the reason。 because of the “limma“ package update 3.32.0,the function length() methods has been removed,these code in "getDiffExpressedGene" function can not get the number of genes(but get the number of list components in the object ).
o length() methods removed all limma data objects (objects of class EList, EListRaw, RGList, MAList or MArrayLM). length(x) will now return the number of list components in the object rather than the number of elements in the expression matrix.aradeger <- topTable(fit2, adjust.method = adj.method, genelist = fit$genes, number = length(fit2))Now,I solve by using limma 3.30，can plot the right heatmap and right result。
Is this the real error causes？if yes，can you solve this problem？(maybe use prod(dim(fit)) to replace length(fit2)）
sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.4 RTCGAToolbox_2.8.0Many thanks！ Dee Chen
PS.I'm a students,English is not very skilled ,If there is something wrong with the content or express, please understanding.