[BioC] error in reading files using HTqPCR
Aashiq Hussain Mirza
mirza at sund.ku.dk
Thu Oct 24 19:27:48 CEST 2013
Hi,
I am trying to read the raw data in HTqPCR package, but it gives me some error which I am unable to interpret. I would really appreciate if you can help me solving this issue.
I run the following commands in R read the Ct values for 768 genes. I explain the column numbers for Ct value (column 5) and genes names (column 6) in the readCtData but it doesn't work. My commands are as follows:
> files_ahm <- read.delim(file.path("/home/simran/qRTPCR_analysis", "files_ahm.txt"))
> raw_ahm <- readCtData(files=files_ahm$File, path="/home/simran/qRTPCR_analysis")
Error in `[.data.frame`(sample, , Ct) : undefined columns selected
In addition: Warning message:
In readCtData(files = files_ahm$File, path = "/home/simran/qRTPCR_analysis") :
384 gene names (rows) expected, got 768
> raw_ahm <- readCtData(files=files_ahm$File, path="/home/simran/qRTPCR_analysis", n.features=768, feature=6, Ct=5)
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file '/home/simran/qRTPCR_analysis/ ': No such file or directory
I have four donor samples (H752, H761, HI1 and HI2) with two conditions (control and Infected) and I have 2 biological replicates for each condition. I am checking expression for 768 genes in each file (two 384 well plates/file). I save their details in the files_ahm.txt as follows:
simran at simran-XPS-L412Z:~$ cat files_ahm.txt
File Treatment
H752_control.txt Control
H752_control_1.txt Control
H752_CVB3.txt Infected
H752_CVB3_1.txt Infected
H761_control.txt Control
H761_control_1.txt Control
H761_CVB3.txt Infected
H761_CVB3_1.txt Infected
HI1_control.txt Control
HI1_control_1.txt Control
HI1_CVB3.txt Infected
HI1_CVB3_1.txt Infected
HI2_control.txt Control
HI2_control_1.txt Control
HI2_CVB3.txt Infected
HI2_CVB3_1.txt Infected
Example of one of the files above is as follows:-
1 Control A01 H752_control 22.73 hsa-miR-7-5p
2 Control A02 H752_control 30.26 hsa-miR-217
3 Control A03 H752_control 30.15 hsa-miR-337-5p
4 Control A04 H752_control 28.23 hsa-miR-328
5 Control A05 H752_control 38.22 hsa-miR-374b-3p
6 Control A06 H752_control 26.03 hsa-miR-143-3p
7 Control A07 H752_control 40.00 hsa-miR-623
8 Control A08 H752_control 37.31 hsa-miR-520c-3p
9 Control A09 H752_control 40.00 hsa-miR-557
10 Control A10 H752_control 32.75 hsa-miR-218-5p
Thank you very much.
A.H. Mirza
PhD student
Center for non-coding RNA in Technology and Health (RTH)
Faculty of Health and Medical Sciences
University of Copenhagen
Groennegaardsvej 3
1870 Frederiksberg C
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