[BioC] AgiMicroRna package error message

Wang, Yonghong (NIH/NCI) [E] wangyong at mail.nih.gov
Wed Jun 16 15:56:26 CEST 2010

Dear Bioconductor users:
I am trying to use AgiMicroRna to perform the microRNA array analysis (Agilent platform) these days, always have some problems. The main problem is the error when  I used the function "filterMicroRna()". Here is the error message:

Error in data.frame(as.character(PROBE_ID), as.character(GENE_ID), as.character(probe.chr),  :
  arguments imply differing number of rows: 795, 0

When I loaded in the data, I used the "read.maimages()" so I can specify which columns to import. I have searched the mailing list and Pedro has suggested to use "readMicroRnaAFE()" to load the data. The first time I tried, for the "genes" information, it include "sequence", "ProbeUID", "ControlType" rather than the required "ControlType, ProbeName, and GeneName". It seems to me the package picked up the column information based on the position rather than column header. After I remove the "sequence, ProbeUID" columns from the raw data files, checked the loaded data, the "genes" information is correct now, but still when I ran the "filterMicroRna() function, same error appear. I have run the sample data set come from the package, everything works fine. I have the following several questions:
First: how can I solve above problem?
Second: I doubt my file format is not exact same to the sample one (probably with more other column information will interfere the correct loading data), if this is the case, who can show me where to download the sample FE file used in the AgiMicroRna package (one is enough, just for the purpose of comparison).
third: there are two functions, one is the tgsNormalization() with the parameter "quantile", another is rmaMicroRna(). I checked the output, they are different. Since RMA is also quantile normalization, I think I miss something here, if anyone can tell me the difference of these two functions, that would be very helpful.
Fourth: This is about the agilent FE file.  How the "gProcessedSignal" file being generated, I mean how this is different to the other intensity information?
Fifth: Since this is my first time to work on the microRNA dataset, any suggests about the data analysis would be very helpful

Thanks in advance

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