Search
Question: how to find up regulated proteins from a label free
1
2.3 years ago by
Nemo80
India
Nemo80 wrote:

hello,

I have 4 samples two control (one biological replicate) and two treated(one biological replicate). I have obtained the intensities for them called LFQ.

Do you think deseq2 is a good way to obtained up regulated proteins ? or should I do it as old school method based on Tueky test etc?

I appreciate any comment

modified 2.3 years ago by Laurent Gatto1.0k • written 2.3 years ago by Nemo80
1
2.3 years ago by
Laurent Gatto1.0k
United Kingdom
Laurent Gatto1.0k wrote:

No, DESeq2 is not appropriate in this case. I would suggest to use limma.

@Laurent Gatto thanks for your message. Is it possible to let me know why? what about other types of proteomics data like SILAC, TMT etc, I guess for them also we cannot use DESeq2, no? is there any paper that used limma for LFQ ?

one technical question, would you remove those genes that have zero for all samples ? i read or do you keep them? (i personally think they have no value) what about the proteins that are identified but their genes are not ? do you remove those proteins too? to be honest it does not harm to keep them , however, I just ask to get different opinion.

Once again thanks

• DESeq2 is only relevant for count data, while LFQ produces continuous data. Same for TMT, SILAC (these are ratios), ... all but spectral counting.
• There is nothing to do with features that have a constant (zero or otherwise) value throughout your samples.