Error when running LFQ data

[RaquelIQS]

There is any possibility of a relative cuantification and doing a heatmap in case of having just one replicate of each sample? How can I fix this to achieve the report without errors like:

• Error in evaluating the argument 'x' in selecting a method for function 'nrow': No finite residual standard deviations
• No finite residual standard deviations

Thanks

Raquel

[hsiaoyi0504]

@RaquelIQS Thanks for the question. We didn't set any limitation of replicates, so should be fine for just one replicate for each condition.

Looks like the error message you got is related to the differential expression analysis. Do you have a more detailed information about your dataset?

[RaquelIQS]

Hi @hsiaoyi0504,

Thank you for your comment, and I apologize for the delayed response. I have three samples of proteins that were attached to nanoparticles. These nanoparticles differ in their composition, so there should be differences in the proteins attached to them (the nanoparticles were incubated in a blood sample). All the samples were processed simultaneously. My idea is to use a heatmap to visualize the differences, like a relative quantification. I can provide you any metadata you need. I'm quite new to this field and entirely self-taught so thank you for the patient and the information.

Raquel

[RaquelIQS]

Im going to keep an eye on this chat. I have already send you some .tsv by email too.

[hsiaoyi0504]

@RaquelIQS Can you send the email again? I couldn't really find it.

[RaquelIQS]

Done, but I think it happens because of the replicates (n = 1)

[RaquelIQS]

Im doing the same with more replicates and there is still an error. I didnt touch the combined protein or the annotation sample file.

[RaquelIQS]

Hi @HSIAO, Thanks for the support. I try to analyze this data but there is a problem that I can't solve by myself. Do you need something else? best regards, Raquel [image: image.png]

…

On Wed, Nov 27, 2024 at 6:12 AM hsiao yi ***@***.***> wrote: @RaquelIQS <https://github.com/RaquelIQS> Can you send the email again? I couldn't really find it. — Reply to this email directly, view it on GitHub <#45 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BKD5RSGIVIXBSLTS7OGABZT2CVIDPAVCNFSM6AAAAABLYFIIPWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMBSHAYTAMZUGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[hsiaoyi0504]

@RaquelIQS I still don't see your email. Where did you send to?