Hello,

I have a protein matrix, and want to use the `justvsn`

function to normalize it.

After normalization, I found all the data are negative, the downstream function only works on positive value.

How can I change the parameter of `vsn`

, them the output can be positive value?

Thank you in advance for great help!

Best,

Yue

Wolfgang Huber

Dear Wolfgang,

Thank you so much for your so detail explanation!

My data is protein SILAC ratio light/heavy data. Just as yo said, the value is too small.

I I tried to normalize the data, and then use

`Deseq2`

to find the diffferentially expressed proteins. I used`VSN`

,`Rlr(performGlobalRLRNormalization)`

,`LoessF (performCyclicLoessNormalization)`

,`median(globalIntensityNormalization)`

. Of course,`vsn2`

has the best perform.Would you please give me some ideas to deal with this kind of data?

Thank you in advance for our great help and really appreciated!

Best,

Yue

`DESeq2`

is strictly for count data, which you can recognize by the fact that they are non-negative integer numbers. It is not intended for (quasi)-continuous data. For general differential abundance testing, please use`limma`

.A workflow of

`vsn2`

followed by`limma`

seems reasonable for your use case, although of course I cannot comment on the suitability (i.e., quality) of your specific data. The package`arrayQualityMetrics`

or at least some of the plots it suggests (e.g. https://www.huber.embl.de/arrayQualityMetrics/Report_for_nCCl4/) may be useful.Hello Wolfgang,

Thank you so much for your great help!

Thank you1

Best，

Yue