Question

Input files for Affymetrix platform

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pbachali ▴ 50

@pbachali-9651

Last seen 5.0 years ago

Hi all, I am trying to analyze a pretty old Affymetrix dataset that has been published on Array Express. I had trouble finding the raw data and I had my supervisor contacted the Array Express team and finally got the raw data. I have analyzed many datasets of Affymetrix platforms. So far I have seen the input files as .CEL or CHP files for Affymetrix. But wit respect to this particular dataset, I have received the .TCT files for 8 samples with two columns "probe" and "signal". Is there any particular package that I could read the files and analyze the dataset?

I would really appreciate your help!!!

Best, Prat

Affymetrix CEL TXT • 926 views

ADD COMMENT • link updated 5.0 years ago by James W. MacDonald 67k • written 5.0 years ago by pbachali ▴ 50

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Never heard of such a thing. What is the array type, and what do the first 5 or so lines of the .tct file look like?

ADD REPLY • link 5.0 years ago James W. MacDonald 67k

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Yes it was strange. It is on HGU133Plus2 platform. And the txt file looks like this:

probe   signal
1007_s_at   6.153
1053_at 7.443
117_at  7.188
121_at  3.986
1255_g_at   2.188
1294_at 11.369
1316_at 3.59
1320_at 2.459
1405_i_at   7.115
1431_at 2.537
1438_at 2.164
1487_at 7.442
1494_f_at   2.231
1552256_a_at    7.903
1552257_a_at    8.102
1552258_at  2.571
1552261_at  2.509
1552263_at  6.692
1552264_a_at    7.144
1552266_at  3.133

Best, Prat

ADD REPLY • link updated 5.0 years ago by James W. MacDonald 67k • written 5.0 years ago by pbachali ▴ 50

score 0 · Answer 1 · 2019-12-11

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 3 days ago

United States

That's not raw data, if by raw you mean the probe intensities. Those are probeset intensities, and are evidently already logged. You could just read in and do some density plots to see if the data are normalised as well.

ADD COMMENT • link 5.0 years ago James W. MacDonald 67k