Hi Christian,
For RNA degradation plot I am getting an error. Please check the following:
load existing ROOT scheme file and ROOT data file
scheme.exon <- root.scheme(paste(scmdir,"Scheme_HuGene20stv1_na35.root",sep="/"))
data.exon <- root.data(scheme.exon, paste("D:/GeneST_Analyse/CELFiles/rootdata/tmp_data_exon_cel.root",sep="/"))
qualification - rlm
rlm.all <- rmaPLM(data.exon, "tmp_exonRLMall", filedir=getwd(), tmpdir="", qualopt="all", option="transcript", exonlevel="affx+core", add.data=FALSE)
(or)
rlm.all <- fitRLM(data.exon,"tmp_exonRLM", qualopt="all", option="transcript", exonlevel="affx+core", verbose=FALSE)
And I get the following error:
Creating new temporary file <D:/GeneST_Analyse/CELFiles/tmp_exonRLMall.root>...
Opening file <D:/GeneST_Analyse/CELFiles/schemes/Scheme_HuGene20stv1_na35.root>
in <READ> mode...
Opening file <D:/GeneST_Analyse/CELFiles/rootdata/tmp_data_exon_cel.root> in <RE
AD> mode...
Preprocessing data using method <preprocess>...
Calculating quality control for <raw> data trees ...
setting selector mask for typepm <9276>
setting selector mask for typepm <9276>
calculating quality controls for <44796> of <51991> units...Finished.
calculating border elements for <X_8__HuGene_2_0_st__raw.brd>...
center of intensity:
positive border elements (x,y) = <0.301687, 0.0508869>.
negative border elements (x,y) = <-0.228422, -0.0683751>.
calculating border elements for <E__HuGene_2_0_st__raw.brd>...
center of intensity:
positive border elements (x,y) = <0.0752159, 0.194383>.
negative border elements (x,y) = <-0.159563, -0.0453415>.
calculating border elements for <GG7__HuGene_2_0_st__raw.brd>...
center of intensity:
positive border elements (x,y) = <0.481647, -0.0256652>.
negative border elements (x,y) = <-0.196879, -0.0731834>.
calculating border elements for <J__HuGene_2_0_st__raw.brd>...
center of intensity:
positive border elements (x,y) = <0.112615, 0.00776396>.
negative border elements (x,y) = <-0.1127, -0.0283493>.
calculating border elements for <O__HuGene_2_0_st__raw.brd>...
center of intensity:
positive border elements (x,y) = <0.119527, 0.141888>.
negative border elements (x,y) = <-0.124044, -0.0194095>.
calculating border elements for <T__HuGene_2_0_st__raw.brd>...
center of intensity:
positive border elements (x,y) = <0.219297, -0.114559>.
negative border elements (x,y) = <-0.144787, 0.0191627>.
Background correcting raw data...
calculating background for <X_8__HuGene_2_0_st_.cel>...
Error: Number of PMs or MMs is zero.
An error has occured: Need to abort current process.
Error in .local(object, ...) : error in rwrapper function 'Preprocess'
Please help me out. Thank you !
Thank you Very much Christian. It worked. Learned many things from the errors.
Hi Christian,
Could you please tell me how RNA degradation plot is calculated? Is it with the mean of every gene or only some genes? Can you please interpret RNA degradation plot?