Question: problems in reading a file in AgiMicroRna package
gravatar for neelakandanbt
18 months ago by
National Institute of Technology
neelakandanbt0 wrote:


I'm using the package AgiMicroRna for analysing my dataset. I have succefully uploded the target file.

After uploading the target file when i tried to read the file im getting the following error while reading the 13th file. 



reading file  1  -  GSM1511526_US10353831_252929710061_S01_miRNA_1010_Sep10_1_1.txt 
reading file  2  -  GSM1511527_US10353831_252929710061_S01_miRNA_1010_Sep10_1_2.txt 
reading file  3  -  GSM1511528_US10353831_252929710061_S01_miRNA_1010_Sep10_1_3.txt 
reading file  4  -  GSM1511529_US10353831_252929710061_S01_miRNA_1010_Sep10_2_1.txt 
reading file  5  -  GSM1511530_US10353831_252929710061_S01_miRNA_1010_Sep10_2_2.txt 
reading file  6  -  GSM1511531_US10353831_252929710061_S01_miRNA_1010_Sep10_2_3.txt 
reading file  7  -  GSM1511532_US10353831_252929710061_S01_miRNA_1010_Sep10_2_4.txt 
reading file  8  -  GSM1511533_US10353831_252929710062_S01_miRNA_1010_Sep10_1_1.txt 
reading file  9  -  GSM1511534_US10353831_252929710062_S01_miRNA_1010_Sep10_1_2.txt 
reading file  10  -  GSM1511535_US10353831_252929710062_S01_miRNA_1010_Sep10_1_3.txt 
reading file  11  -  GSM1511536_US10353831_252929710062_S01_miRNA_1010_Sep10_1_4.txt 
reading file  12  -  GSM1511537_US10353831_252929710062_S01_miRNA_1010_Sep10_2_2.txt 
reading file  13  -  GSM1511538_US10353831_252929710062_S01_miRNA_1010_Sep10_2_3.txt 
Error in Newagi[[a]][, n] <- obj[, columns[[a]]] : 
number of items to replace is not a multiple of replacement length 2  -  

          Then i tried to upload the 13th file alone seperately and it was showing the following error.

the command and the output is given. i dont know what went wrong kindly help me in this.


reading file  1  -  GSM1511538_US10353831_252929710062_S01_miRNA_1010_Sep10_2_3.txt 



dd$TGS: 'gTotalGeneSignal'  

dd$TPS: 'gTotalProbeSignal'  

dd$meanS: 'gMeanSignal'  

dd$procS: 'gProcessedSignal'  


Warning message:

In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :

  embedded nul(s) found in input


ADD COMMENTlink modified 18 months ago by Axel Klenk920 • written 18 months ago by neelakandanbt0

Hi Neela,

I don't know the answer to your problem I'm afraid. The only thing I can think of is when I ran these arrays a few years back there was an issue initially with the feature extraction on the scanner. It essentially defaulted to saving a minimal reduced output rather than a `full` output. That might be where your problems are? Have a dig around the software and make sure you're saving the full results.


Good luck

ADD REPLYlink written 18 months ago by j.iremonger0
Answer: problems in reading a file in AgiMicroRna package
gravatar for Axel Klenk
18 months ago by
Axel Klenk920
Axel Klenk920 wrote:

Dear Neela,

Agilent's reduced output is lacking the 'gMeanSignal' column and this will cause an issue. I'm not sure it is the source of your problem, though, since I'd expect it to affect *all* files rather than just the 13th.

You can inspect the source code of AgiMicroRna::readMicroRnaAFE by typing it like that, i.e., without parentheses,

and you will see that it essentially passes your target data.frame on to a function read.agiMicroRna but is also hardcoding the column names.

To find out if the missing 'gMeanSignal' column is causing your problem, try:

dd <- AgiMicroRna:::read.agiMicroRna(targets1.micro, columns = list(TGS = "gTotalGeneSignal",
        TPS = "gTotalProbeSignal", meanS = "gMedianSignal", procS = "gProcessedSignal"),
        other.columns = list(IsGeneDetected = "gIsGeneDetected",
            IsSaturated = "gIsSaturated", IsFeatNonUnifOF = "gIsFeatNonUnifOL",
            IsFeatPopnOL = "gIsFeatPopnOL", BGKmd = "gBGMedianSignal",
            BGKus = "gBGUsed"), annotation = c("ControlType",
            "ProbeName", "GeneName"), verbose = TRUE)

Note the three colons and the change from 'gMeanSignal' to 'gMedianSignal'. Also note that it's a hack. No warranty. :-)

Good luck,

 - axel

ADD COMMENTlink modified 18 months ago • written 18 months ago by Axel Klenk920
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