Question: Support for import of custom matrix data in the ddCt R package
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gravatar for mohammedtoufiq91
27 days ago by
mohammedtoufiq910 wrote:

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 R analysis import qrtpcr • 50 views
ADD COMMENTlink modified 27 days ago by Zhang, Jitao David110 • written 27 days ago by mohammedtoufiq910
Answer: Support for import of custom matrix data in the ddCt R package
1
gravatar for Zhang, Jitao David
27 days ago by
Switzerland
Zhang, Jitao David110 wrote:

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 COMMENTlink written 27 days ago by Zhang, Jitao David110

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 REPLYlink written 27 days ago by mohammedtoufiq910
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