I'm not sure the bond out of the pins from the die makes any difference, I think you need to double check the A-J designators and the associated pins on the device in the schematic.
My annotations to the table relate the the GPIO assignments described in the code.
GPIO_InitStructure.GPIO_Pin = GPIO_Pin_0; /* Configure GPIOA.0 as analog input (CH A) */
GPIO_Init(GPIOA, &GPIO_InitStructure);
GPIO_InitStructure.GPIO_Pin = GPIO_Pin_4; /* Configure GPIOA.4 as analog input (CH B) */
GPIO_Init(GPIOA, &GPIO_InitStructure);
GPIO_InitStructure.GPIO_Pin = GPIO_Pin_0; /* Configure GPIOB.0 as analog input (CH C) */
GPIO_Init(GPIOB, &GPIO_InitStructure);
GPIO_InitStructure.GPIO_Pin = GPIO_Pin_1; /* Configure GPIOB.1 as analog input (CH D) */
GPIO_Init(GPIOB, &GPIO_InitStructure);
GPIO_InitStructure.GPIO_Pin = GPIO_Pin_0; /* Configure GPIOC.0 as analog input (CH E) */
GPIO_Init(GPIOC, &GPIO_InitStructure);
GPIO_InitStructure.GPIO_Pin = GPIO_Pin_1; /* Configure GPIOC.1 as analog input (CH F) */
GPIO_Init(GPIOC, &GPIO_InitStructure);
GPIO_InitStructure.GPIO_Pin = GPIO_Pin_2; /* Configure GPIOC.2 as analog input (CH G) */
GPIO_Init(GPIOC, &GPIO_InitStructure);
GPIO_InitStructure.GPIO_Pin = GPIO_Pin_3; /* Configure GPIOC.3 as analog input (CH H) */
GPIO_Init(GPIOC, &GPIO_InitStructure);
GPIO_InitStructure.GPIO_Pin = GPIO_Pin_4; /* Configure GPIOC.4 as analog input (CH I) */
GPIO_Init(GPIOC, &GPIO_InitStructure);
GPIO_InitStructure.GPIO_Pin = GPIO_Pin_5; /* Configure GPIOC.5 as analog input (CH J) */
GPIO_Init(GPIOC, &GPIO_InitStructure);
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A copy/paste/remove-the-proprietary-names error. I've relabeled the GPIO comments to match the order that the code is really in.
When I apply voltages to each of my inputs, I'm getting the correct changes but the data in the output array is in the wrong spot when I have 13 inputs.Expected for 13 inputs and actual with 12 inputs based on ADC_RegularChannelConfig(): Ch_A, Ch_B, Ch_C...Actual with 13 inputs: Ch_J, CoreTemp, Vrefint, Vbat, Ch_A, Ch_B, ....
I didn't want to leave this thread hanging.: I finally got back to this with a newer build of code -- the ADC section had been turned off since it wasn't required for what we were using. Everything is working now. Interestingly, going back to the version that had the offsets in the output still shows the data incorrectly. Nothing stands out as being different.
This is concerning and I'll have to look further into it.