Issue with AT

[EricaSalguero]

I am trying to calculate the AT for Qiagen kits: 26plex and Argus X12, using positive control samples. But the software shows this message:

Error in set(x, j = name, value = value) : Supplied 100 items to be assigned to 97 items of column 'Sample.Mean'. If you wish to 'recycle' the RHS please use rep() to make this intent clear to readers of your code.

But the software has not problem with Promega and Applied Biosystems kits. I have checked the file already and it is fine. can you please help me?

[OskarHansson]

Could you attach or send me some data and instructions how to replicate the error?

[EricaSalguero]

Hi,

I send the files I'm working with. The 26plex file is not working. But the PPF6C file is fine. I'm just following the instructions to calculate the AT. I've been working with the software for a long time, so I have been able to analyze several kits before.

Thanks for your help

Erica Salguero

El mié, 28 ago 2024 a las 23:29, Oskar Hansson @.***>) escribió:

Could you attach or send me some data and instructions how to replicate the error?

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Dye/Sample Peak Sample File Name Marker Allele Size Height Area Data Point [...] B,284 CN1_G03.hid 73.81 6 19 3991 B,285 CN1_G03.hid 74.22 7 30 3997 B,286 CN1_G03.hid AM OL 75.39 25 303 4014 B,287 CN1_G03.hid AM OL 76.28 24 238 4027 B,288 CN1_G03.hid 77.54 3 12 4045 B,289 CN1_G03.hid 78.1 3 9 4053 B,290 CN1_G03.hid 78.66 6 29 4061 B,291 CN1_G03.hid AM Y 79.86 4 30 4078 B,292 CN1_G03.hid AM OL 80.95 11 76 4093 B,293 CN1_G03.hid 81.46 5 18 4100 B,294 CN1_G03.hid 82.12 8 29 4109 B,295 CN1_G03.hid 82.78 5 22 4118 B,296 CN1_G03.hid 83.73 11 63 4131 B,297 CN1_G03.hid 84.89 7 50 4147 B,298 CN1_G03.hid 85.4 4 18 4154 B,299 CN1_G03.hid 85.91 6 28 4161 B,300 CN1_G03.hid 86.43 5 24 4168 B,301 CN1_G03.hid 86.94 6 47 4175 B,302 CN1_G03.hid 88.25 6 34 4193 B,303 CN1_G03.hid 88.98 7 37 4203 B,304 CN1_G03.hid 89.85 6 36 4215 B,305 CN1_G03.hid 90.27 6 44 4221 B,306 CN1_G03.hid 91.44 5 25 4238 B,307 CN1_G03.hid TH01 4 91.85 7 37 4244 B,308 CN1_G03.hid 92.26 5 20 4250 B,309 CN1_G03.hid TH01 OL 92.81 7 63 4258 B,310 CN1_G03.hid 93.63 6 54 4270 B,311 CN1_G03.hid 94.65 4 20 4285 B,312 CN1_G03.hid 95.75 9 43 4301 B,313 CN1_G03.hid 96.09 5 19 4306 B,314 CN1_G03.hid 96.71 5 36 4315 B,315 CN1_G03.hid 97.74 4 14 4330 B,316 CN1_G03.hid 98.35 6 35 4339 B,317 CN1_G03.hid 99.11 6 53 4350 B,318 CN1_G03.hid 100.15 7 32 4365 B,319 CN1_G03.hid 100.88 7 41 4375 B,320 CN1_G03.hid 101.54 5 23 4384 B,321 CN1_G03.hid TH01 6.3 102.36 4 30 4395 [...]

[OskarHansson]

It seems like the data is incomplete. Could you please send it to me by mail, as attached files?

[EricaSalguero]

Hi,

I have sent the email to @.***

Thanks

El jue, 29 ago 2024 a las 7:33, Oskar Hansson @.***>) escribió:

It seems like the data is incomplete. Could you please send it to me by mail? image.png (view on web) https://github.com/user-attachments/assets/4b66d60b-c853-4cad-8c90-53108d4774a1

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[OskarHansson]

Sorry for taking so long. Before analysing the data, I split the positive and negative controls in separate datasets. For the PPF6C_3500_UA_muestras_CP, I could confirm the error. However, PPF6C_3500_UA_muestras_CN, X26PLEX_3500_UA_muestras_CP, X26PLEX_3500_UA_muestras_CN worked. It seems like you have very little noise signals for the PPF6C_3500_UA_muestras_CP. The error was triggered by missing data in samples CP1_ESC_TC5_C07 (Orange), CP3_ALPV_TC4_A06 (Orange), and CP5_ESC_TC1_G04 (Red). After removing these samples using trim function the analysis worked. I will try to fix this bug. To solve your issue: 1) check that you have analysed the data in GeneMapper with the correct settings for analytical threshold. You should use a peak amplitude threshold = 1 RFU to collect all signals. 2) In STR-validator, check all analysis settings to calculate analytical threshold. Especially, if you use the "Mask high peaks" option, make sure that the threshold ("Mask all peaks above (RFU)") is not too high, resulting in few noise signals. You can preview a plot of each sample by selecting it from the drop-down menu. Let me know if this help.