Runtime: isoformSwitchAnalysisCombined()

[Betül Bozkurt]

Hi Kristoffer,

I am running the isoform switch analysis using the isoformSwitchAnalysisCombined() function. I have 569 samples (404 Alzheimer's disease patients & 165 controls). My design matrix has the following columns: Sample ID, condition (AD/control), gender, age of death, and pmi. The last three are the confounding variables. I have already imported kallisto abundance files and created the mySwitchAnalyzeRlist. 

I was wondering how long will it take to run the analysis for 569 samples with ~160,000 transcripts? I am using a desktop computer with the following specifications:

Processor: Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz   2.60 GHz  (2 processors)

Installed RAM: 32 GB

System type: 64-bit operating system, x64-based processor

Many thanks in advance,

Betul

[Betül Bozkurt]

Hi again Kristoffer,

The analysis was run for weeks then I got this error message: "Error in fitBeta(ySEXP = ySEXp, ................... , : std::bad_alloc

Could you help me with this issue? 

Many thanks in advance,

Betul

8 Ocak 2023 Pazar tarihinde saat 21:31:43 UTC-5 itibarıyla Betül Bozkurt şunları yazdı:

[Kristoffer Vitting-Seerup]

I have good news for you. If you update to IsoformSwitchAnalyzeR 2.1.8 from the github you will have access to use isoformSwitchTestSatuRn() which can handle large datasets!

Also when you run so many samples, I'd recommend using the step-by-step workflow instead of the high-level one.

[lu lu]

Hey,

I total have 13 samples, I tried isoformSwitchTestSatuRn, but it failed, it shows:

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'which': 'list' object cannot be coerced to type 'double' In addition: There were 17 warnings (use warnings() to see them)

How could I fix it?

Thanks so much!

Best,

Lu

[Betül Bozkurt]

Thanks for your help! I tried the isoformSwitchTestSatuRn() but got the following error message which is the same error message as Lu posted earlier:

Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 'which': 'list' object cannot be coerced to type 'double'

In addition: Warning messages:
1: glm.fit: algorithm did not converge
2: glm.fit: algorithm did not converge
3: glm.fit: algorithm did not converge
4: glm.fit: algorithm did not converge
5: Zero sample variances detected, have been offset away from zero 

How can I fix this? 

Many thanks in advance,

Betul

10 Mart 2023 Cuma tarihinde saat 11:01:31 UTC-5 itibarıyla lu lu şunları yazdı:

[Kristoffer Vitting-Seerup]

Could you post this error on github - I need the help from somebody who does not use the google group :-)

[Betül Bozkurt]

Sure Kristoffer, I opened an issue about the error on github few minutes ago. Thank you!

13 Mart 2023 Pazartesi tarihinde saat 08:59:30 UTC-4 itibarıyla Kristoffer Vitting-Seerup şunları yazdı: