Question: Phyloseq to DESeq2 Help
0
gravatar for crharris
25 days ago by
crharris0
crharris0 wrote:

I'm trying to do some contrasting in DESeq2 and I keep getting an error that my object is empty.

Here's my metadata table:


Sample Data: [21 samples by 5 sample variables]: Sample Site Treatment Impacted AllParams Indv Cass2 Lake Uncontaminated No CLUn CLUn2 Cass1 Lake Uncontaminated No CLUn CLUn1 Cass16 Lake Oil Yes CLOil CLOil16 Cass17 Lake Oil Yes LOil CLOil17 Cass12 Lake Plume Yes LPlume LPlume12 Cass15 Lake Plume Yes LPlume LPlume15 Cass6 Lake Plume Yes LPlume LPlume6 B14 Bem Uncontaminated No BUncon BUn14 B15 Bem Uncontaminated No BUncon BUn15 B115 Bem Oil Yes BOil BOil115 B124 Bem Oil Yes BOil BOil124 Bem26 Bem Oil Yes BOil BOil26 B75 Bem Plume Yes BPlume BPlume75 B76 Bem Plume Yes BPlume BPlume76 B71 Bem Plume Yes BPlume B_Plume71

I subset it so that it now looks like this:


Sample Data: [4 samples by 5 sample variables]: Sample Site Treatment Impacted AllParams Indv B14 Bem Uncontaminated No BUn BUn14 B15 Bem Uncontaminated No BUn BUn15 Cass1 Lake Uncontaminated No LUn LUn1 Cass2 Lake Uncontaminated No LUn L_Un2

The name of my subset file is Uncontaminated_phyla

From the start: clbbacphyloseq <- import_mothur(shared file & constaxonomy file)

clbbacmetadata <- data.frame(read .csv)

clbbacmetadataphyloseq <- sampledata(data.frame(Site = clbbacmetadata["Site"], Treatment = clbbacmetadata["Treatment"], Impacted = clbbacmetadata["Impacted"], AllParams = clbbacmetadata["AllParams"], Indv = clbbacmetadata["Indv"]))

clbbacfullphyloseq <- mergephyloseq(clbbacphyloseq, clbbacmetadata_phyloseq)

clbbacfullphyla <- taxglom(clbbacfull_phyloseq, taxrank = "Rank2")

Uncontaminatedphyla <- subsetsamples(clbbacfullphyla, Treatment=="Uncontaminated") sampledata(Uncontaminated_phyla)

ddsUncontaminatedphyla <- phyloseqtodeseq2(Uncontaminatedphyla, ~Indv) sampledata(ddsUncontaminatedphyla)

When I run phyloseqtodeseq2, my object is empty: Error in access(object, "samdata", errorIfNULL) : samdata slot is empty.

deseq2 • 105 views
ADD COMMENTlink modified 24 days ago by Michael Love25k • written 25 days ago by crharris0

I'M SO SORRY!!!!!!!!!!!!!!!

When I pasted over my tables, I swear they didn't look like that!

ADD REPLYlink written 25 days ago by crharris0

Original metadata table:

Sample Data: [21 samples by 5 sample variables]: Sample Site Treatment Impacted AllParams Indv Cass2 Lake Uncontaminated No CLUn CLUn2 Cass1 Lake Uncontaminated No CLUn CLUn1 Cass16 Lake Oil Yes CLOil CLOil16 Cass17 Lake Oil Yes LOil CLOil17 Cass12 Lake Plume Yes LPlume LPlume12 Cass15 Lake Plume Yes LPlume LPlume15 Cass6 Lake Plume Yes LPlume LPlume6 B14 Bem Uncontaminated No BUncon BUn14 B15 Bem Uncontaminated No BUncon BUn15 B115 Bem Oil Yes BOil BOil115 B124 Bem Oil Yes BOil BOil124 Bem26 Bem Oil Yes BOil BOil26 B75 Bem Plume Yes BPlume BPlume75 B76 Bem Plume Yes BPlume BPlume76 B71 Bem Plume Yes BPlume B_Plume71

Here's my subset table:

Sample Data: [4 samples by 5 sample variables]: Sample Site Treatment Impacted AllParams Indv B14 Bem Uncontaminated No BUn BUn14 B15 Bem Uncontaminated No BUn BUn15 Cass1 Lake Uncontaminated No LUn LUn1 Cass2 Lake Uncontaminated No LUn L_Un2

ADD REPLYlink modified 25 days ago • written 25 days ago by crharris0

SORRY AGAIN!

I tried to redo and fix it, but i guess I can't. but the main thing is that my 5 sample variable are: 1)Site 2)Treatment 3)Impacted 4)All_Params and 5) Indv

ADD REPLYlink written 25 days ago by crharris0

If you surround your table with three backticks like ``` it should format more neatly. You can also achieve this by pressing the 'code' button with 1's and 0's on it.

ADD REPLYlink written 25 days ago by Mike Smith3.9k
Answer: Phyloseq to DESeq2 Help
0
gravatar for Michael Love
24 days ago by
Michael Love25k
United States
Michael Love25k wrote:

This is a phyloseq issue, as you haven't gotten the data into DESeq2 yet.

Try making a new post (use backticks as Mike Smith suggests also for code) and tagging that package instead of DESeq2 to notify the appropriate package maintainers.

ADD COMMENTlink written 24 days ago by Michael Love25k
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