I performed a transcriptome analysis (Clariom D Array, Affymetrix) of two groups of subjects (human tissue) by using Transcriptome Analysis Console (TAC; Affymetrix) and Partek software and same cutoff (n=20; FC greater than 1.5 and P value less than 0.05). However, the overlap between differential expressed genes between both software was quite low.
someone has some comment about why this may be happening?
Thanks
Normal. Algorithms happen to be that different.
Perhaps find a bioinformatician who can still do it with Bioconductor.
This will be at least better publishable :)
And why not RNA-seq to get really a whole overview of the transcriptome?
For a window user,
These two
Geneious : https://www.geneious.com/
CLC Genomics: https://www.qiagenbioinformatics.com/products/clc-genomics-workbench/
are good.
Thank you
Honestly i prefer the TAC analysis more, as it is quite easy to use and analzye your transcriptome data. If u use two types of software, you are going to get different readings. So stick to the technique you have used to analyze your human tissue. For me I used Affymetrix kit to perform microarray, so I used TAC for analysis.
of course i can understand that different algorithms could give different results, but i think that at least I could expect a good degree of overlap. Otherwise, how can I be sure that my findings are real?
I analysed recently the same data with R (biocoductor/bioinformatic) and the results agree a little bit more with TAC (not fully)
thabks for the comments
PD: absoliutely true that TAC is more user friendly
I have not analysed Affy, with small exceptions, since RNA-seq was available in a stable form, so some 8 years or so... But in the "old times" Affy did say often "we are not software company" and were waiting for the academia to design the methods and wrap them in software. Good luck anyway :)
As far as i understand, arrays are just screening tools, the only way for u to be sure of the results is to select a few target genes and do a PCR analysis. The results has to be tallied not in the fold change but at least the trend is there. I hope this helps :)
Does anybody have the TAC analysis tool 3.0 version? Because I need to the conversion of miRNA CEL files to txt. TAC4.0 version does not realize that.
Faizatul Isyraqiah Mario Ezquerra Michal Okoniewski
hi merve, sorry i don't have it. You can ask your previous affymetrix technical specialist to get the file. Usually they will give both versions 3.0 and 4.0
Leila Khorraminezhad Unfortunately No! I tried to use it with parallel and with wine but couldn't get it to work on my M1 mac with 8Gb. and knowing ThermoFisher I think they will not provide native Mac support. I think you can use it with parallel if you allocate 8Gb RAM for emulation.
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