Made a pDATA manually for HTqPCR procedure
0
0
Entering edit mode
Marcelo Laia ▴ 450
@marcelo-laia-2007
Last seen 3.1 years ago
Brazil

I have a set of seven files from runs on 48 low-throughput qpcr system. So, our runs have 48 max samples. In fact, we have 30 reactions per run. Our file is like this:

File1.csv

1   10-A1-C C9  1   IDH Endogenous Control  12.6929092407226
2   10-A1-C C10 1   IDH Endogenous Control  12.4841232299805
3   10-A1-S C11 2   IDH Endogenous Control  18.4506340026855
...
30  9-A1-S  F2  15  IDH Endogenous Control  17.3977642059326

File2.csv

1   10-A1-C A1  1   UBQ Endogenous Control  11.66
2   10-A1-C A2  1   UBQ Endogenous Control  11.7372970581054
3   10-A1-S A3  2   UBQ Endogenous Control  16.82
...
30  9-A1-S  C6  15  UBQ Endogenous Control  17.3474025726318

File3.csv

1   10-A1-C C9  1   CDPK26  Target  16.9320430755615
2   10-A1-C C10 1   CDPK26  Target  17.0587520599365
3   10-A1-S C11 2   CDPK26  Target  16.5248744964599
...
30  9-A1-S  F2  15  CDPK26  Target  16.9789012908935

...

File7.csv

1   10-A1-C C9  1   MYB Target  12.5751647949219
2   10-A1-C C10 1   MYB Target  12.959545135498
3   10-A1-S C11 2   MYB Target  10.3745765686035
...
30  9-A1-S  F2  15  MYB Target  12.228588104248

First column -> id (1 until 30)

Second column -> sample identification (10 = genotype; A1 = region 1; C = symptoms). We have three genotypes (10, 3 and 9); two regions (A1 and A2) and with symptoms and without. So, we have theses RNA samples: 10-A1-C, 10-A1-S, 10-A2-S, 3-A1-C and 9-A1-S.

third column -> well plate

fourth column -> technical replicates 1 or 2

fifth column -> gene name

sixth column -> feature type (endogenous or target)

seventh column -> Ct

I read my files like this:

files <- read.delim("files.txt")
raw  <- readCtData(files = files$File, n.features = 30,
                   column.info=list(feature = 5, type = 6, position = 3,
                                    Ct = 7), n.data = 1)

Now, I would like to do the appropriate phenoData file for, on downstream analysis do a proper statistical contrasts set up.

So, could you help me?

Thank you so much!

Marcelo

HTqPCR phenoData esetVis pData • 710 views
ADD COMMENT

Login before adding your answer.

Traffic: 850 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