Unable to use the function named read.agiMicroRna()
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topijush ▴ 10
@topijush-14730
Last seen 2.4 years ago

Please help me to use the function named read.agiMicroRna(). Getting the error given below.

> library("AgiMicroRna")
> dd=AgiMicroRna:::read.agiMicroRna(targets.micro,
+                     columns=list(TGS="gTotalGeneSignal",
+                                  TPS="gTotalProbeSignal",
+                                  meanS="gMeanSignal",
+                                  procS="gProcessedSignal"),
+                     other.columns=list(IsGeneDetected="gIsGeneDetected",
+                                        IsSaturated="gIsSaturated",
+                                        IsFeatNonUnifOF="gIsFeatNonUnifOL",
+                                        IsFeatPopnOL="gIsFeatPopnOL",
+                                        BGKmd="gBGMedianSignal"),
+                     annotation = c( "ControlType", "ProbeName","SystematicName"),
+                     verbose=TRUE)
reading file  1  -  257015615988_1_1.txt 
Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected

AgiMicroRna • 322 views
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Entering edit mode
Axel Klenk ▴ 990
@axel-klenk-3224
Last seen 20 hours ago
Switzerland

Dear topijush,

please check your input file 25701561598811.txt and make sure that it contains the columns you're providing to the function in arguments columns, other.columns, and annotation -- the error message is trying to tell you that at least one of these cannot be found.

BTW, your message is a bit hard to read for potential helpers, isn't it?

Hope this helps.

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