Question

Support for import of custom matrix data in the ddCt R package

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mohammedtoufiq91 ▴ 10

@mohammedtoufiq91-17679

Last seen 5 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 • 805 views

ADD COMMENT • link updated 4.7 years ago by Zhang, Jitao David ▴ 120 • written 4.7 years ago by mohammedtoufiq91 ▴ 10

score 1 · Answer 1 · 2019-08-20

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Zhang, Jitao David ▴ 120

@zhang-jitao-david-5737

Last seen 4.1 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 • link 4.7 years ago Zhang, Jitao David ▴ 120

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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 • link 4.7 years ago mohammedtoufiq91 ▴ 10