search

honzee / RNAseqCNV

R package for large-scale CNV analysis from RNA-seq
MIT License
11 stars 8 forks source link

An unresolved error #25

Open jieyu-He opened 9 months ago

jieyu-He commented 9 months ago

When I perform batch analysis and my own built-in standard sample analysis, I always get the following error

Error in vecseq(f, len, if (allow.cartesian || notjoin || !anyDuplicated(f__, : Join results in 247187 rows; more than 224126 = nrow(x)+nrow(i). Check for duplicate key values in i each of which join to the same group in x over and over again. If that's ok, try by=.EACHI to run j for each group to avoid the large allocation. If you are sure you wish to proceed, rerun with allow.cartesian=TRUE. Otherwise, please search for this error message in the FAQ, Wiki, Stack Overflow and data.table issue tracker for advice.

honzee commented 9 months ago

Hi,

thank you for trying out our package. Apparently there is some problem with joining data within the package. Firstly, I would make sure, that all your count files have the same gene sets. The error might be suggesting, that the your custom standard count files have different number of genes than the other files.

However, from the message, I am unable to determine the exact cause of the error. I would therefore also ask some questions.

  1. Does it work normally with the built-in standard?
  2. Could you send me the send me the RNAseqCNV_wrappper command you used to run the analysis?
  3. Could you send me the header of your metadata and one of your count files?

Best, Jan

jieyu-He commented 9 months ago

Hello, glad you got my reply. I did not get any errors when using method one (single sample analysis). But when I use method two (batch analysis), the above error will appear. Similarly, when I set up the standard sample using method 1 to analyze, the above error also occurred. 11 Cannot run Run the code to view the pictures I posted

jieyu-He commented 9 months ago

I checked and the gene sets in my count files are all the same, no problem. There is no problem with these samples during individual analysis and the results can be obtained.

honzee commented 9 months ago

Hi jieyu,

I am sorry I couldn't help you. Have you managed to solve issue? If yes, please let me know how.

Jan