try this. It read in all the data and discards the lines not required.
> # read in the data and delete lines not required
> data_in <- readLines(textConnection("HEAD OF MYDATA
+ * Block Type = Array Card Block
+ * Calibration Background is expired = No
+ * Calibration Background performed on = 2014-12-02 11:27:49 AM PST
+ * Calibration FAM is expired = No
+ * Calibration FAM performed on = 2014-12-02 12:00:20 PM PST
+ * Calibration ROI is expired = No
+ * Calibration ROI performed on = 2014-12-02 11:20:40 AM PST
+ * Calibration ROX is expired = No
+ * Calibration ROX performed on = 2014-12-02 12:11:21 PM PST
+ * Calibration Uniformity is expired = No
+ * Calibration Uniformity performed on = 2014-12-02 11:43:43 AM PST
+ * Calibration VIC is expired = No
+ * Calibration VIC performed on = 2014-12-02 11:51:59 AM PST
+ * Chemistry = TAQMAN
+ * Experiment Barcode =
+ * Experiment Comments =
+ * Experiment File Name = F:\2015-04-13 Gastro array 59 Luigi - plate
3.eds
+ * Experiment Name = 2015-04-13 171216
+ * Experiment Run End Time = 2015-04-13 18:07:57 PM PDT
+ * Experiment Type = Comparative
+ * Experiment User Name =
+ * Instrument Name = 278882033
+ * Instrument Serial Number = 278882033
+ * Instrument Type = ViiA 7
+ * Passive Reference = ROX
+ * Quantification Cycle Method = Ct
+ * Signal Smoothing On = false
+ * Stage/ Cycle where Analysis is performed = Stage 3, Step 2
+
+ [Amplification Data]
+
+ Well \tCycle \tTarget \tName \tRn
+ \t1 \t1 \tAdeno 1 \t0.82
+ \t1 \t2 \tAdeno 1\ \t0.93
+ \t2 \t1 \tAdeno 2 \t0.78"))
>
> indx <- grep("Amplification Data", data_in) + 1
> data_in <- tail(data_in, -indx) # delete lines
> read.table(text = data_in, header = TRUE, sep = '\t')
Well Cycle Target Name Rn
1 NA 1 1 Adeno 1 0.82
2 NA 1 2 Adeno 1 0.93
3 NA 2 1 Adeno 2 0.78
>
>
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.
On Mon, Apr 27, 2015 at 5:20 PM, Luigi Marongiu <marongiu.lu...@gmail.com>
wrote:
> Dear Duncan,
> thank you for your reply,
> I tried to read the file using skip and nrows but it did not work.
> Here i am pasting the code I wrote and the head of the file i need to
> read. Probably the error is due to the fact that the column "well" has
> duplication, but how can i add a row column with unique row names? How
> can I overcome this error?
> Best regards
> Luigi
>
> CODE
> raw.data<-read.table(
> mydata,
> header=TRUE,
> row.names=31,
> dec=".",
> sep="\t",
> skip = 30,
> nrows = 17281,
> row.names = 1:17281
> )
>
>
> HEAD OF MYDATA
> * Block Type = Array Card Block
> * Calibration Background is expired = No
> * Calibration Background performed on = 2014-12-02 11:27:49 AM PST
> * Calibration FAM is expired = No
> * Calibration FAM performed on = 2014-12-02 12:00:20 PM PST
> * Calibration ROI is expired = No
> * Calibration ROI performed on = 2014-12-02 11:20:40 AM PST
> * Calibration ROX is expired = No
> * Calibration ROX performed on = 2014-12-02 12:11:21 PM PST
> * Calibration Uniformity is expired = No
> * Calibration Uniformity performed on = 2014-12-02 11:43:43 AM PST
> * Calibration VIC is expired = No
> * Calibration VIC performed on = 2014-12-02 11:51:59 AM PST
> * Chemistry = TAQMAN
> * Experiment Barcode =
> * Experiment Comments =
> * Experiment File Name = F:\2015-04-13 Gastro array 59 Luigi - plate 3.eds
> * Experiment Name = 2015-04-13 171216
> * Experiment Run End Time = 2015-04-13 18:07:57 PM PDT
> * Experiment Type = Comparative Cт (ΔΔCт)
> * Experiment User Name =
> * Instrument Name = 278882033
> * Instrument Serial Number = 278882033
> * Instrument Type = ViiA 7
> * Passive Reference = ROX
> * Quantification Cycle Method = Ct
> * Signal Smoothing On = false
> * Stage/ Cycle where Analysis is performed = Stage 3, Step 2
>
> [Amplification Data]
>
> Well \tCycle \tTarget \tName \tRn
> \t1 \t1 \tAdeno 1 \t0.82
> \t1 \t2 \tAdeno 1\ \t0.93
> ...
> \t2 \t1 \tAdeno 2 \t0.78
> ...
>
> On Mon, Apr 20, 2015 at 12:17 PM, Duncan Murdoch
> <murdoch.dun...@gmail.com> wrote:
> > On 20/04/2015 3:28 AM, Luigi Marongiu wrote:
> >> Dear all,
> >> I have a flat file (tab delimited) derived from an excel file which is
> >> subdivided in different parts: a first part is reporting metadata,
> >> then there is a first spreadsheet indicated by [ ], then the actual
> >> data and the second spreadsheet with the same format [ ] and then the
> >> data.
> >> How can I import such file using for instance read.table()?
> >
> > read.table() by itself can't recognize where the data starts, but it has
> > arguments "skip" and "nrows" to control how much gets read. If you
> > don't know the values for those arguments, you can use readLines() to
> > read the entire file, then use grep() to recognize your table data, and
> > either re-read the file, or just extract those lines and read from them
> > as a textConnection.
> >
> > Duncan Murdoch
> >
> >> Many thanks
> >> regards
> >> Luigi
> >>
> >> Here is a sample of the file:
> >> * Experiment Barcode =
> >> * Experiment Comments =
> >> * Experiment File Name = F:\array 59
> >> * Experiment Name = 2015-04-13 171216
> >> * Experiment Run End Time = 2015-04-13 18:07:57 PM PDT
> >> ...
> >> [Amplification Data]
> >> Well Cycle Target Name Rn Delta Rn
> >> 1 1 Adeno 1-Adeno 1 0.820 -0.051
> >> 1 2 Adeno 1-Adeno 1 0.827 -0.042
> >> 1 3 Adeno 1-Adeno 1 0.843 -0.025
> >> 1 4 Adeno 1-Adeno 1 0.852 -0.015
> >> 1 5 Adeno 1-Adeno 1 0.858 -0.008
> >> 1 6 Adeno 1-Adeno 1 0.862 -0.002
> >> ...
> >> [Results]
> >> Well Well Position Omit Sample Name Target Name Task
> >> Reporter Quencher RQ RQ Min RQ Max CT Ct Mean Ct
> >> SD Quantity Delta Ct Mean Delta Ct SD Delta Delta Ct
> >> Automatic Ct Threshold Ct Threshold Automatic Baseline
> >> Baseline Start Baseline End Efficiency Comments Custom1
> >> Custom2 Custom3 Custom4 Custom5 Custom6 NOAMP
> >> EXPFAIL
> >> 1 A1 false P17 Adeno 1-Adeno 1 UNKNOWN FAM
> >> NFQ-MGB Undetermined false
> >> 0.200 true 3 44 1.000 N/A N
> >> Y
> >> 2 A2 false P17 Adeno 40/41 EH-AIQJCT3 UNKNOWN FAM
> >> NFQ-MGB Undetermined
> >>
> >> ______________________________________________
> >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >>
> >
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
