Support for import of custom matrix data in the ddCt R package
1
0
Entering edit mode
@mohammedtoufiq91-17679
Last seen 9 weeks ago
United States

Hi,

I would like to know if I can import the data into the ddCt package in the matrix format for the analysing the qRTPCR data. If possible, how could this be done?

I have a .txt file with 260 genes (rows) and 27 samples (columns).

Best Regards,

Toufiq

ddCt import analysis R qRTPCR • 965 views
ADD COMMENT
1
Entering edit mode
@zhang-jitao-david-5737
Last seen 4.7 years ago
Switzerland

Hi, here's David, co-author and maintainer of the package. Do you mind giving me a minimal example? Thanks.

Besides data, information such as house-keeping genes and reference samples are helpful.

ADD COMMENT
0
Entering edit mode

Thank you David.

I am currently working with the Biomark Fluidigm qRT-PCR data. This is a raw threshold cycle (Ct) data, there are a total of 264 test genes + 8 housekeeping genes and 27 samples (columns)in the .txt format. These 27 samples are grouped into 3 timepoints (i.e Timepoint_1 = 7, Timepoint_2 = 9, and Timepoint_3 = 11). My reference samples are Timepoint_1 samples and HKs are geometric mean of 8 Hks to form Psuedogene. Basically, I would like to import the data, map the annotation/sample grouping data. After this calculate DCt, Negative DCt, DDCt, and 2(DDCt) and other statistical analysis. I would like to import this data into the ddCt package since my file is not in the standard SDM format which is required by the ddCt package. I am interested in knowing the specific function/command to load this type of data and perform the other steps.

ADD REPLY

Login before adding your answer.

Traffic: 441 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6