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7 weeks ago

bbibi.msbi20rcms
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0

Hi,

I have downloaded TCGA data generated from TOIL RNA-seq pipeline. Basically, it is log2(x+0.001) transformed transcript-level expression values (FPKM) matrix. Link to dataset

I intend to analyze isoform switching using IsoformSwitchAnalyzeR which won't work with log2 transformed data or negative values.

So I need to revert the Log2 (FPKM+0.001) to FPKM to remove the negative values but I'm not sure how?

Will taking antilog using 2^(FPKM_log2T_value) work? If not, then is there any other way?

Your help will be much appreciated.

Hi,

I never used

`IsoformSwitchAnalyzeR`

so I'm not familiar with the kind of input it needs and if it'll work with`FPKM`

.To revert

`Log2 (FPKM+0.001)`

to`FPKM`

you need to do (as you pointed out):`2^(FPKM_log2T_value)`

The only thing that you forgot was to subtract the

`pseudocount`

0.001. Thus to revert to`FKPM`

just subtract the value of 0.001 to`2^(FPKM_log2T_value)`

.You can easily check this in

`R`

(or any other software or just a simple calculator):You may have problems to revert the

`log2(FPKM+0.001)`

due to rounded values, but you'll have a close value to the original.Although, as I mentioned, I don't know what kind of input

`IsoformSwitchAnalyzeR`

requires, if for instance it accepts fraction numbers or not, so you need to read carefully their documentation.I hope that helps,

AntÃ³nio

Thanks so much for the reply.

hey, I just noticed that subtracting the pseudocount leads a few values (e.g. when fpkm_log2 is -9.9658) to be negative.

So I guess I'll have to check if the value after taking antilog is less than 0.001 then I won't be subtracting the pseudocount. On the contrary, if value after antilog turns out to be >0.001, subtraction will be performed. Does that seem alright?