Despite huge challenges, Abbott Laboratories (ABT - Get Report) Chairman and CEO Miles White said Wednesday he remains upbeat on the outlook for two big deals the company has embarked upon in the last year, the just-closed $33 billion acquisition of St. Jude Medical Inc. and the recently restructured agreement to acquire Alere (ALR) for $500 million less than the companies' original plan.

White addressed the mergers' pitfalls in a call with analysts to discuss Abbott's first quarter results.

Shares of the medical device, nutritional products and pharmaceutical maker rose 0.37% Wednesday to $43.59, up 16 cents.

Concerns hovering over the mergers were among the factors pushing the shares down. The biggest concern about the St. Jude deal is a warning letter from regulators last week about quality control at a California manufacturing plant.

A Food and Drug Administration inspection of the Sylmar, Calif. acquired from St. Jude began soon after Abbott closed the deal in January. The FDA made 483 observations requiring corrective actions at the plant. The FDA raised concerns about whether Good Manufacturing Practices were followed at the plant, where the Merlin home monitor and the Fortify, Unify and Assura implantable cardiac defibrillators are produced.

White said the warning letter "is clearly a disappointment but not unanticipated." The company had been working with St. Jude and FDA officials about the plant's issues for some time.

White could not estimate when the problems would be cleared up but said there already has been "a fair amount of dialogue with FDA officials about the matter."

He also said that Abbott itself has a good reputation at the FDA regarding manufacturing controls and that should give regulators confidence that the company can address the plant's problems adequately.

Ultimately, "the impact will depend on our response and how effective it is," he said. "We've got excellent people on that."

White added that Abbott is not limiting its internal review of plant manufacturing process to the Sylmar facility but also wants to make sure other plants are following GMP processes too.

White also was positive about the long-term prospects for integrating Alere into the fold despite a lengthy dispute between the two companies over their merger plans.

Abbott and Alere announced April 14, that they'd agreed to restructure their merger contract, ending litigation between the two healthcare companies. Abbott will now pay $51 per Alere share, or $5.3 billion in equity value.

In their original merger agreement, announced Feb. 1, 2016, Abbott agreed to pay $56 per share, an equity value of $5.8 billion, with an enterprise value of $7.9 billion. Disputes quickly arose, however, with Abbott on Dec. 7 filing a suit against Alere in the Delaware Court of Chancery seeking to terminate the agreement. Abbott argued that Alere had experienced material adverse events which warranted termination as defined in their contract; Alere countered that the suit was baseless and only wanted to back out of the deal because it wanted to buy St. Jude instead.

Despite the battle, White said Monday that Alere still offers an attractive business to Abbott. "We like the space; we like the expansion of our diagnostics business."

He characterized the settlement with Alere as "fair."

The deal still must be approved by the Federal Trade Commission and he said some divestitures will have to be made.

"We will divest a couple of pieces," White said. "When we announced the deal, that wasn't clear."

White said the most challenging part of completing the Alere deal isn't obtaining FTC approval but winning over Alere shareholders, who are taking a haircut.

"The long pole in the tent isn't the divestiture but the shareholder vote," he said.

In a note Tuesday Leerink analyst Danielle Antalffy said the firm has a $48 price target on the shares but remains cautious due to concern about the company's ability to hit synergy targets for its just-completed acquisition of St. Jude as well as the restructured acquisition of Alere.

Antalffy said the major risks to Abbott's valuation include the possibility that the Alere acquisition fails to close, the potential for slower growth and increasing competition for major products, including Abbott's Xience drug-eluting stent, any product recalls or manufacturing warning letters that could lead to costly remediation costs or hinder sales.