[BioC] error in reading files using HTqPCR

Aashiq Hussain Mirza mirza at sund.ku.dk
Thu Oct 24 19:27:48 CEST 2013


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 

More information about the Bioconductor mailing list